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Practical Guide
to the Identification
of Selected Diseases
of Wheat and
Practical Guide
to the Identification
of Selected Diseases
of Wheat and
L. Gilchrist-Saavedra, G. Fuentes-Davila
and C. Martinez-Cano
CIMMYT is an internationally funded, nonprofit scientific research and training organization. Headquartered
in Mexico, the Center works with agricultural research institutions worldwide to improve the productivity and
sustainability of maize and wheat systems for poor farmers in developing countries. It is one of 16 similar
centers supported by the Consultative Group on International Agricultural Research (CGIAR). The CGIAR
comprises over 50 partner countries, international and regional organizations, and private foundations. It is co-
sponsored by the Food and Agriculture Organization (FAO) of the United Nations,. the International Bank for
Reconstruction and Development (World Bank), the United Nations Development Programme (UNDP), and
the United Nations Environment Programme (UNEP).
Financial support for CIMMYT's research agenda currently comes from many sources, including the
governments of Australia, Austria, Belgium, Canada, China, Denmark, France, Germany, India, Iran, Italy,
Japan, the Republic of Korea, Mexico, the Netherlands, Norway, the Philippines, Spain, Switzerland, the United
Kingdom, and the USA, and from the European Union, the Ford Foundation, the Inter-American Development
Bank, the Kellogg Foundation, the OPEC Fund for International Development, the Rockefeller Foundation, the
Sasakawa Africa Association, UNDP, and the World Bank.
Responsibility for this publication rests solely with CIMMYT.
Correct citation: Gilchrist-Saavedra, L., G. Fuentes-Davila, and C. Martinez-Cano. 1997. Practical Guide to the
Identification of Selected Diseases of Wheat and Barley. Mexico, D.E: CIMMYT.
ISBN: 968-6923-82-9
AGROVOC descriptors: Wheats; Barley; Plant diseases; Bacterioses; Fungal diseases; Viroses; Nematoda;
Identification; Methods.
AGRIS category codes: H2O
Dewey decimal classification: 633.1193
Edited by: Alma McNab
Design and layout: Juan J. Joven, Eliot Sanchez P. and Marcelo Ortiz S. Printed in Mexico.
Table of Contents
Preface vi
Collecting samples 1
Preserving samples 1
Basic requirements of a plant pathology lab 3
Basic equipment 3
Maintaining a microbe-free environment 5
Sterilization 6
Disinfection 7
Culture media 7
Types of media 7
Deciding which culture media to use 8
Lab practice 8
Media preparation 8
How to prepare moist chambers 16
Preparing specimens for observation under the microscope 17
Determining inoculum concentration 19
Greenhouse inoculation 21
Introduction 24
The rusts 24
Monitoring the leaf rust population 25
Questions 28
Smuts and bunts 28
Identifying loose smut and Kamal bunt 29
Inoculation methods 29
Introduction 31
Identification of spot blotch caused by Helminthosporium sativum 31
Symptoms and isolation of the fungus 32
Identification of tan spot caused by Helminthosporium tritici-repentis 32
Symptoms and isolation of the fungus 33
Identification of Helminthosporium spp., causal agents of barley net and
spot blotch 33
Symptoms and isolation of the fungus 33
Identification of leaf blotch caused by Mycosphaerella graminicola
(Septoria tritici) and glume blotch caused by Lepthosphaeria nodorum (Septoria nodorum) 34
Symptoms and isolation of the fungus 34
Identification of head scab of wheat caused by Fusarium spp. 35
Identification of black point caused by Alternaria alternata, A. triticina
Symptoms and isolation of the fungus 35
Inoculum preparation and field inoculation 35
Introduction 37
and/or Helminthosporium sativum 37
Symptoms and isolation of the pathogen 37
Identification of Rhynchosporium secalis, causal agent of barley scald 37
Symptoms and isolation of the pathogen 38
Introduction 40
Symptoms caused by Fusarium and Helminthosporium 40
Symptoms and isolation of Fusarium 40
Isolation and identification of Helminthosporium 43
Symptoms of Pythium, Gaeumannomyces and Rhizoctonia 44
Pythium 44
Gaeumannomyces graminis var. tritici (syn. Ophiobolus graminis), take-all 44
Rhizoctonia 45
Isolation of Pythium, Gaeumannomyces and Rhizoctonia 45
Identification of Pythium 47
Method for inducing zoospore production 48
Identification of Gaeumannomyces 48
Identification of Rhizoctonia 48
Identification of Sclerotium rollsii 48
Introduction 49
Soil nematodes: Identification of parasitic and saprophytic species 49
Sampling techniques 49
Methods for isolating nematodes from soil and plant tissue samples 51
Comparing two methods for isolating nematodes from soil and plant tissue 52
Identification of Meloidogyne species 52
Preparing perineal patterns of Meloidogyne females 52
Introduction 54
Identifying a bacterial disease 54
Pathogenicity test 56
Biochemical and physiological tests 57
Introduction 60
Barley yellow dwarf virus 60
Identification of BYDV aphid vectors 61
BYDV transmission 61
Barley stripe mosaic virus 62
BSMV transmission 62
Detecting seed transmission of the virus 63
Appendix 64
This practical guide is intended for use in identifying some wheat and barley diseases and their causal
agents. It can also help readers learn to handle those pathogens in labs, in the field, and in greenhouses.
The guide is not intended to be a comprehensive treatise on wheat and barley pathogens. Instead it
targets the most important pathogens that affect small grain cereals in developing countries, since
economic losses in those countries are more significant than in other cereal-producing areas of the world.
The guide is intended for researchers working on plant pathology in support of small grain cereal
improvement programs aimed at generating disease-resistant germplasm. However, it sho';1ld also be
useful for technicians and extension workers who do not have a plant pathologist to help them identify
The authors wish to thank Drs. Etienne Duveiller, Dennis A. Lawn and Monica Mezzalama for their
contribution to the bacteria, nematode, and virus chapters, respectively. Also, the authors wish to thank
Dr. Jesse Dubin for reviewing the manuscript; Alma McNab for editing it; Marta Larios for typing the
information; Ana Maria Sanchez for taking the photographs; and Miguel Mellado and Eliot Sanchez for
preparing the figures and formatting the publication.
General Overview
Collecting samples
Collections of disease samples are extremely useful in studying disease symptoms and
forming representative pathogen populations. The isolates can later be used for
artificially inoculating host genotypes in selecting for resistance.
When collecting field samples, it is important to take into account such factors as crop
growth stage at the time of collection, plant part to be collected, lesion development,
and prevailing environmental conditions. Collection data such as location, date, crop,
and variety, as well as symptom description, should be specified for each sample.
Preserving samples
Samples can be placed in paper or plastic envelopes, unless the weather is hot and
humid, because these conditions favor saprophyte development. Samples should be
dried as soon as possible. In general, plastic bags are used only in emergencies or when
other types of containers are unavailable.
A press is recommended for drying the samples (see below for instructions on how to
build one). Place plant tissue in the press in such a way that symptoms are readily
visible. When samples consist of leaves whose adaxial and abaxial sides are different,
two leaves are used, one face up and the other face down. If a press is not available,
samples can be laid out in the same manner on newspaper or blotters and a weight
placed on top.
The dried sample and its corresponding data are transferred to a diagnostic sheet. If the
necessary equipment is available, samples are observed under the microscope or
isolates made, to start the identification process. All observations made during this
process (signs and symptoms, morphology) should also be added to the diagnostic
sheet (Figure 1; Zillinsky, 1983). In this way, a reference sample of the most important
diseases in a region can be made that includes data which later will facilitate pathogen
identification and help to understand local phytosanitary problems.
How to build a press. A press consists of two base parts made of a durable, strong
material such as wood (Figure 2a, b). Nail together four wood strips 1.5 inches wide to
form a 12" x 18" (30.5 cm x 46 cm) rectangle, as shown in Figure 2b. (measurements can
be adjusted as needed). Place newspaper between the two bases to dry plant samples.
To apply and maintain constant pressure on the samples, use two I" (2.54 cm) wide
leather strips for tightening the press (Figure 2b).
Figure 1. Disease identification.
Sample Causal Agent
If samples are to be used for starting a collection of the pathogen population, dry them
for 48 h, making sure they are properly identified. After drying, samples are transferred
to paper envelopes, which in tum are placed inside plastic bags. Plastic bags should be
sealed to keep out moisture and stored at 4C.
Basic requirements of a plant
pathology laboratory
Laboratory work is extremely important in plant pathology. Basic research is conducted
in the lab, plant pathogens are isolated and identified, and inoculum is produced for
doing artificial inoculations in both field and greenhouse.
Basic equipment
A lab should be equipped with sterilizers, autoclaves (gas or electric), ovens, isolation
chambers, incubators, microscopes, stereoscopes, and water baths, among other things.
Autoclaves. Used for sterilizing with moist heat. Water vapor inside an autoclave can
reach a temperature of 120C and 181b/in
(1.4 kg/cm
) pressure. The heat source may
be electric or, in the case of a pressure cooker, a gas burner. A pressure cooker works like
a big autoclave but has the advantage of being very low-cost. Both devices are used
primarily for sterilizing artificial media but can also handle soil, sand, vermiculite, or
any other substrate used for growing plants and microorganisms.
Figure 2a. Parts of a press. b. Finished press.
Ovens. An oven provides a wide temperature range by means of dry heat. It is used for
drying plant or soil samples at constant temperatures and sterilizing glassware at high
Isolation chambers. Laminar flow chambers (LFCs) have an air flow mechanism that
filters outgoing air. This avoids contamination by microorganisms and provides sterile
conditions. Microvoids work much the same way as LFCs but are smaller and cheaper.
If LFCs and microvoids are not available, a small room with no air currents and a gas or
alcohol burner (to avoid contamination) may serve as an isolation chamber.
Incubators. An incubator can be calibrated to a wide range of light/ temperature
combinations. Incubators are extremely useful for artificially growing many plant
pathogens requiring specific light/temperature conditions. Partial incubators can be
built by hand out of wood; near-ultraviolet (NUV) light is supplied by fluorescent
tubes, and a light control is used to regulate light/darkness cycles (Figure 3a, b). Since
temperature cannot be controlled in this type of incubator, it should be located in a
place where temperature is 15-22C, the range at which many plant pathogens develop.
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Refrigerators. Essential mainly for storing plant material, cultures, artificial media,
reagents, etc.
Water bath. This device consists of a container that maintains water at a constant
temperature. Water baths have many uses. For example, Erhlenmeyer flasks containing
freshly sterilized culture medium can be placed in a water bath at 46C to cool it before
pouring into Petri dishes. Water baths are essential for measuring growth of some
organisms in liquid media at specific temperatures, and have other uses in bacteriology
and virology.
Microscopes and stereoscopes. Essential for the identification, classification, and
quantification of plant pathogens, as well as for observing symptoms and lesions and
evaluating experiments.
Maintaining a microbe-free environment
A microbe-free environment is essential in a plant pathology laboratory, since it is
required for most of the work that goes on there. For this reason, it is important to have
LFCs, microvoids, or isolation chambers in which to work with specific pathogens
without the risk of contamination. Contamination may come from various sources such
as utensils and human hands. Work utensils (needles, forceps, etc.) should be sterilized
after every use by cleaning them with alcohol and flaming. Hands should be washed
and cleaned with alcohol before working under sterile conditions.
Care must be taken because some fungi present as saprophytes in many tissue samples
or in the lab environment may grow and reproduce rapidly. Plant tissue samples
brought into the lab should be kept to a minimum and above all should not be handled
as inoculum within the lab. It is very difficult to control contamination in the lab once it
has occurred.
Mite contamination is also common, especially in Petri dishes that have been deformed
as a result of dry heat sterilization. Mites can invade poorly sealed dishes or test tubes
and contaminate the contents. This type of contamination is hard to control. It is
therefore essential that plant materials collected in the field be properly disinfected; in
addition, care must be taken when handling cultures from other labs, tubes and plates
should be well sealed, and incubators should be fumigated. If mite contamination does
occur, incubators and ovens must be emptied completely and turned on for a couple of
hours at a temperature above 50C; repeat the procedure two days later.
To avoid contamination problems, all plant materials entering the lab must be controlled.
In addition, work tables should be routinely cleaned with alcohol or sodium hypochlorite.
Techniques for isolating, identifying, and multiplying inoculum, and biological and
physiological studies of pathogens require pure cultures. A microbe-free environment is
therefore essential. Sterilization of utensils, equipment, and work areas means that all
living cells (microorganisms) must be eliminated or inactivated. This is done by
physical or chemical means that irreversibly destroy the protoplasmic structure of cells.
Selection of the sterilization method depends upon efficiency and safety requirements,
taking into account toxicity, availability, cost, and the effects of the sterilizing agent on
the physical and chemical properties of the object to be sterilized.
The most common physical methods are heat, ionic radiation, and ultrafiltration (for
some liquids). Heat sterilization is used when materials to be sterilized are not damaged
by high temperatures under dry or moist conditions.
Dry heat. Used to sterilize utensils made of glass, metal, and certain kinds of plastic.
This type of sterilization requires higher temperatures and longer exposure than moist
heat processes, and also hot air ovens that produce uniform heat. The time of exposure
is inversely proportional to the temperature; for example, 1 hr at 180C, 2 hr at 170C, 4
hr at 150C, and 12-16 hr at 120C. Start counting sterilization time when maximum
temperature is reached. Glassware should be completely dry, otherwise it may break.
Graduated materials should not be sterilized by this method because their dimensions
may change. To avoid breakage, sterilized materials should be left in the oven until they
reach room temperature.
Moist heat. The most convenient method for sterilizing most materials, moist heat is
quick and has greater penetrating power at lower temperatures in a shorter period of
time. It requires using water vapor pressure inside an autoclave. For most purposes,
exposure is 20 minutes at 121C or 30 minutes at 115C. It is important to expel all the
air from the chamber before closing the valve; if not, temperature will not rise. Exposure
is calculated starting from the time desired temperature and pressure are reached (15
or 1.4 kg/cm
). Moist heat can be used on liquids, plastics (although not on all of
them), soil, sand, and vermiculite.
Ultraviolet light. Ultraviolet light is used for sterilization because it kills most
microorganisms. While it is recommended for plastic materials, it cannot penetrate
glass. Ultraviolet systems must be installed in a closed chamber to avoid exposure, since
it is harmful to the eyes.
Ultrafiltration. Used when proteins and sugars (which break down easily if exposed to
high temperatures) must be kept intact. Filters act as barriers for microorganisms. Their
size and consistency vary depending on the microorganisms to be filtered.
When contaminants must be removed from objects that cannot be subjected to
sterilization, the best option is disinfection with chemicals such as mercuric chloride,
sodium hypochlorite, alcohol, and ethylene bromide. The most commonly used
substances are sodium hypochlorite and alcohol at concentrations that vary depending
upon the object to be sterilized. When isolating pathogens, chemicals are useful for
removing contaminants from samples, for example, 1% sodium hypochlorite for plant
material (leaves, roots) and 3-5% for seeds. Alcohol (70%) is widely used for disinfecting
surfaces or even plant material. '
Culture media
In identifying plant diseases, potential causal agents need to be isolated. In order to do
this, microorganisms (mainly fungi and bacteria) are isolated in artificial media, where
they are purified and stimulated to sporulate and produce inoculum. The resulting
inoculum is used for artificial inoculations to produce disease symptoms, a process
which is necessary for pathogen identification (Koch's postulates). The Appendix
summarizes information on culture media used for growing and preserving cereal
Types of media
Culture media are solutions for growing one or more microorganisms. They may be
solid or liquid; the only difference is that solid ones contain agar, are prepared in flasks,
petri dishes, or test tubes and are used for isolating and maintaining fungi and bacteria.
Liquid media are used mainly for increasing fungal and bacterial populations, and
determining their physiologic properties either in stationary fashion or in a shaker. This
allows greater aeration, which promotes uniform growth and helps maintain
pathogenicity. Based on their composition, different media may be classified as:
Non-nutrient media. Used to obtain monosporic cultures, isolate pathogens from plant
tissue, and force sporulation of some fungi. Water-agar is the most common example of
this type of medium.
Nutrient solutions. May be natural, semi-synthetic, or synthetic. Natural solutions only
contain plant tissue (leaf, root, pod, and grain) in small pieces or crushed, and have
been sterilized. Semi-synthetic solutions contain both natural (animal or plant extracts
and processed plant products such as maize flour and oat bran) and synthetic
compounds. Synthetic solutions are composed entirely of chemicals and can be
reproduced for specific experiments.
Some semi-synthetic and synthetic media are available in dehydrated form to which
water is added. Only distilled water should be used to mix culture media.
Deciding which culture media to use
The type of culture medium that should be used will depend on the objectives of your
study, e.g., isolation, physiological or biological studies (which require the production of
sexual and asexual structures), or inoculum production. Choosing the appropriate
medium is very important, since the pathogen's infectivity and capacity to produce
propagules will depend greatly on it. Another important factor in culture media is the
pH level which, in the case of fungi, is generally 5.8-6.5, but may vary depending on the
Some physical factors (aeration, light, humidity, and temperature) affect pathogen
growth and sporulation. Minimum and maximum points as well as optimum levels for
growth and sporulation will vary according to the pathogen under study. Sporulation
usually requires conditions unfavorable to vegetative growth.
Lab practice
Media preparation
When preparing culture media, paying attention to details will make your work more
efficient. For example, fill containers only halfway to keep the contents from soiling the
lids during sterilization; flasks should be covered with cotton, aluminum foil or both.
After sterilization is completed, do not remove covers until sterile conditions are met or
a burner is available. To cool the medium, place in a water bath at 46C for 30 minutes,
but if a water bath is not available, you should wait until the medium cools somewhat
before pouring into the Petri dishes. (A practical way of determining when to pour is to
touch the container with the back of the hand; if it feels warm, it's ready to pour.) This
keeps condensation, which promotes contamination, from forming inside the plates.
Pouring media into Petri dishes or test tubes should be done in a sterile chamber or a
draft-free room using a burner. It's best to heat the mouth of the flask, avoid opening
the dishes too widely, and try to keep a minimum distance between flask and Petri dish
to avoid contamination (Figure 4).
The medium should be poured 24-48 h before use, to allow any condensation to dry.
Another way to avoid condensation is to stack the Petri dishes one on top of another as
they are filled with medium (Figure 4).
When tubes, flasks or other types of containers are to be used, heat can be used to
homogenize the medium. Pour the medium into the containers (Figure Sa), cover,
sterilize, and let cool. Test tubes are usually cooled in a slanted position to provide
greater area for growth (Figure Sb).
Culture media most commonly used for isolating and growing fungi. To identify and study
pathogens, it is necessary to isolate and grow them. Thus practicing the preparation of
some of the more commonly used media is recommended.
Figure 4. How to pour culture media and avoid condensation.
&- ....ll a
Figure Sa. Pouring medium into test tubes. b. Cooling medium-filled test tubes at a slant to
provide larger growth surface.
1. Water-agar: Often used to isolate and germinate spores, obtain monosporic
cultures, and verify inoculum viability.
Agar 15-20 g
Distilled water 1000 ml
Preparation: Using a flask (half full), dissolve agar in water and sterilize.
2. Potato-dextrose-agar (PDA): Most widely used for isolating, multiplying, and
storing fungi because it is suitable for a large number of species.
Sliced potatoes 250 g
Dextrose 10 g
Agar 20g
Distilled water 1000 ml
Preparation: Boil the potatoes in 500-700 ml of distilled water for 15-20 minutes.
Filter through cheesecloth; pour into a flask and add dextrose, agar, and enough
water to reach 1000 ml. Seal flask with cotton or aluminum foil and sterilize. Let
cool and pour into Petri dishes (halfway). Stack dishes one on top of another to
avoid condensation.
In many countries, dehydrated PDA is available on the market; add distilled water
according to the manufacturer's instructions and sterilize as follows. Place 9.75 g
dehydrated PDA in a 500-ml flask and add 250 ml distilled water. Heat suspension
to homogenize; pour 4-5 ml of medium into each test tube using a syringe. Seal
tubes and sterilize; let cool at a slant until solid (Figure 5b). If a syringe is not
available, use a funnel on a metal stand. Adjust a piece of flexible tubing to the end
of the funnel, regulating outflow by means of a pinch clamp. Measure out the
desired amount of medium into one of the test tubes, to use as a guide during
pouring (Figure Sa).
3. V-8 agar: Useful for inducing sporulation in many fungi. V-8 juice is made by the
Campbell Soup Co. and Herdez, a Mexican firm, among others; it contains tomato,
celery, beet, parsley, lettuce, spinach, and watercress extracts. Since there are
differences among brands, comparative testing on each species is recommended. If
canned V-8 juice is not available, it can be replaced with a medium containing leaf
extract (such as the following), especially for testing Helminthosporium tritici-repentis
and H. teres.
V-8 juice 200ml
Calcium carbonate 3g
Agar 15-20 g
Distilled water 800ml
Preparation: Place agar and calcium carbonate in a flask; add the juice and mix with
water to complete 1000 ml. Seal the flask and sterilize. Stir the medium before
pouring to keep the juice from precipitating. This medium may be prepared at
different concentrations by adjusting the amount of juice used.
4. Leaf extract medium: Used primarily for stimulating growth and formation of
asexual structures in some fungi. Leaves of different crops may be used, depending
on the pathogen.
Agar 15-20 g
Distilled water 1000 ml
Fresh leaves (wheat,
oats, barley, etc.) 100 g
Sucrose 10 g
Preparation: Boil leaves for 20-30 min and filter the water. Add filtrate to agar and
mix with water to 1000 ml. Sterilize and pour into Petri dishes or test tubes.
5.4-4-4 agar-malt-yeast medium: Frequently used for isolating and multiplying
Septaria tritici.
Malt extract 4g
Yeast extract 4g
Sucrose 4g
Agar 18 g
Streptomycin 0.1 g
Distilled water 1000 ml
Preparation: Place all ingredients except the antibiotic in distilled water. Mix well
and sterilize for 20 min. Add the antibiotic while the medium is still warm, then
pour into Petri dishes or test tubes.
6. Medium for Septoria nodorum: Recommended for the development and growth
of S. nodarum pycnidia.
Malt extract 3g
Yeast extract 2g
0 0.5 g
Agar 20g
Streptomycin 0.1 g
Distilled water 1000 ml
Preparation: Mix all the ingredients and sterilize for 20 min; add the antibiotic
while the medium is still warm, then pour into Petri dishes or test tubes.
7. Medium used to increase Fusarium graminearum: If Chinese bean is available, this
medium is inexpensive and very efficient for producing large amounts of inoculum.
Chinese beans 20 g
Distilled water 1000 ml
Preparation: Boil the beans in water for 20 min; filter the solution and sterilize the
filtrate for 20 min in 500 ml flasks (just half full).
Inoculum increase: Inoculate the liquid medium and shake for five days.
8. Lima bean agar: This medium is utilized for Rynchosparium secalis isolation and
inoculum increase, as well as for fungi that attack the roots and crown. It can be
prepared from lima beans or commercial preparations can be purchased.
Lima beans 8g
Agar 15-18 g
Distilled water 1000 ml
Preparation: Boil the lima beans in water for 20 min; filter the infusion, add the agar
and sterilize for 20 min.
9. Sacarose-yeast liquid medium: Used only for increasing Septaria tritici, and only
if a shaker is available and existing conditions favor daily inoculum applications,
since viability is lost after five days.
Sacarose 10 g
Yeast extract 10 g
Distilled water 1000 g
Preparation: Mix the components and sterilize for 20 min in 250-ml flasks. Let the
medium cool, then inoculate and shake continuously during the entire incubation
period. Use the inoculum after five days.
10. Leaf segment medium: Appropriate for stimulating the formation of sexual
structures in some fungi.
Agar 15-20 g
Distilled water 1000 ml
Small pieces of fresh leaves
(try different species)
Preparation: Dissolve the agar in water. Place the leaf pieces in Petri dishes and sterilize.
Pour the sterilized water-agar into the plates.. When the agar has nearly solidified, place
5-10 leaf pieces on each plate so they will stay in the top part of the agar. The pieces are
inoculated with the fungus under study and periodically observed.
Media for fungal conservation. In preserving and managing fungal cultures, the number
and frequency of isolate transfers should be reduced to once every six months. To avoid
changes in pathogenicity, isolates should be maintained in as natural a substrate as
possible (for example, wheat leaves for Pythium; wheat seed for Fusarium and other
fungi). Preservation procedures vary depending on the pathogen under study.
1. Grains: A great variety of grains are used to preserve certain fungi. In this way,
the fungi maintain their stability and do not lose their virulence or their sporulating
capacity, as they would in some synthetic media. The type of grain used depends
on the fungus you're working with.
The grain is soaked in distilled water for 24 hours; drain the excess water, and place
the grain in test tubes, flasks or bottles. Close the lids without tightening, and
sterilize in the autoclave for 2 h. Incubate for 48-72 h at room temperature (22C) to
make sure there are no contaminating fungi or bacteria. After incubation, inoculate
the grain with a pure culture of the pathogen, and incubate for 7-10 days or more if
necessary to obtain good sporulation. During incubation, move the tubes or flasks
every two days, striking them against your hand to keep a compact mass from
forming and to facilitate fungal growth.
For isolate conservation, place the tubes or flasks in plastic bags and store in a
refrigerator. For inoculum multiplication, extract and suspend culture in sterile
distilled water and store at 4-5 DC, once it reaches the appropriate growth stage.
Wheat, barley, triticale and sorghum grain can be used as a substrate, depending on
the pathogen's affinity. Media based on grain are commonly used for species of
Fusarium and Helminthosporium. Gaeumannomyces graminis can be maintained and
multiplied in sterilized oat seed following the procedure described above.
2. Sterile soil: Sterilize moist soil for 2 h in test tubes or flasks; repeat after an
interval of at least 24 h. This allows any resistance structures that were not
eliminated during the first sterilization phase to subsequently germinate (also
recommended for grains). After sterilization, test tubes or flasks are ready to be
inoculated with pure cultures.
3. Sterile water with leaf pieces: Very useful for preserving cultures of Phythium
spp. This pathogen is kept in a wheat leaf and water medium. Wheat seedling
leaves (5-6 leaves, 2 cm long) are air-dried and suspended in 9 ml distilled water in
test tubes. Cover the tubes with cotton plugs and sterilize in an autoclave. Transfer
the cultures aseptically by removing a piece of agar and allow them to grow for
several days at room temperature; seal tubes with paraffin and keep at 4-5C.
Isolates thus prepared can be maintained for a year or more without doing
additional transfers.
To re-initiate growth, take a small leaf segment from the cultures and place in com
meal agar (CMA). Not all species can survive long periods stored in this way;
therefore, if you are working with Pythium, isolates should be transferred every six
months until the viability of the species under study is determined.
4. Leaf extract medium: Used specifically for preserving Septoria tritid isolates for
long periods without changes in virulence.
Wheat leaves 30g
Bactoagar 20g
Streptomycin 0.1 g
Distilled water 1000 ml
Preparation: Leaves are crushed in a mortar or blender with water, then filtered
through cheesecloth to separate larger fragments; add agar and sterilize for 20
minutes. When the medium is warm, add the streptomycin and mix gently using a
rotating motion to homogenize, taking care not to splash the medium on flask walls
and lids. Pour into Petri dishes, meting out just enough medium to cover the
bottom of the plates. For long-term storage, inoculate the medium by placing
Septoria conidia in the center of the plate. Stack several plates together and cover
with aluminum foil; keep them at 20-25C until the water from the medium
evaporates (approximately three months). Mature pycnidia should have formed at
the end of that time. Isolates thus prepared can be maintained for long periods (up
to three years) at 4-6C.
To re-activate the culture, pycnidia are extracted and placed in a medium
appropriate for Septoria growth. However, it should be noted that not all isolates
are able to form pycnidia in this medium.
5. Preservation on dried, infected leaves: Helminthosporium tritici-repentis, H. teres
and Rynchosporium secalis are difficult to maintain in culture media because their
pathogenicity and sporulation capacity can be drastically reduced or irreversibly
destroyed. To avoid this problem, inoculate the isolates onto susceptible cultivars
under controlled conditions. Leaves with developing lesions are dried at room
temperature for 48 h and then stored at 4C. Helminthosporium tritici-repentis can
remain viable for six months under these conditions. Isolates of R. secalis are placed
in a tight plastic container and stored in a freezer at -15C. This protocol should be
tested on other species that also cause foliar lesions.
Barnes, E.H. 1968. Atlas and Manual of Plant Pathology. New York: Plenum Press.
French, E.R., and Teddy, T.H. 1982. Metodos de investigaci6n fitopato16gica. 1a edici6n.
1a. reimpresi6n. San Jose, Costa Rica: ilCA.
Tuite, J. 1969. Plant Pathological Methods. Fungi and Bacteria. Department of botany
and plant pathology, Purdue University, Lafayette, Indiana.
The Commonwealth Mycological Institute. 1968. Plant Pathologist's Pocketbook.
Commonwealth Agricultural Bureau.
Zelibovitch, N., and Z. Eyal. 1989. Maintenance of virulence of Septoria tritici cultures.
Mycological Research 92(3):361-364.
Zillinsky, EJ. 1984. Common Diseases of Small Grain Cereals: A Guide to Identification.
Mexico, D.E: CIMMYT. 141 pp.
How to prepare moist chambers
Moist chambers are a quick, direct way of stimulating sporulation and helping to
identify the causal agents of some diseases. They are especially useful for identifying
microorganisms that show rapid growth on the host and compete well with
saprophytes in a moist chamber.
Preparation: Cut leaves or stems into small pieces and tape them onto a sterile slide.
Sterilize pieces with 5% sodium hypochlorite for 30-60 seconds; rinse samples in sterile
water to remove hypochlorite and dry on paper towels. !t's a good idea to leave a few
pieces untreated because some pathogens are very sensitive to sterilization. Do not
select heavily damaged tissue to avoid saprophytic organisms. Place filter paper disk on
the bottom of the Petri plate and moisten it thoroughly with sterile water (Figure 6a).
Place the slide on the paper disk (Figure 6b). Close the plate and seal it with parafilm to
hold in moisture (Figure 6c). Incubate plate at 18-22C under alternating cycles of light
and darkness (10 h light/14 h darkness) (many fungi will not develop to the
reproductive stage without this alternating light/ darkness regimen).
Open the plate after 24, 48 and 72 h of incubation. Place the slide under the dissecting
microscope, and observe the structures that have developed on the lesion. If necessary,
take a tiny portion of the fungal growth with adissecting needle and put it in a drop of
water on a slide. Cover the slide, being careful not to form air bubbles (use a dissecting
needle as an aid). Look for mycelium, conidia, conidiophores, and other fungal
structures under the compound microscope. If no structure is visible, close and seal the
plate again to make sure it doesn't lose moisture and continue observation. Draw any
observed structure.
Figure 6 a, b, c. How to prepare a moist chamber.
Preparing specimens for observation under the microscope
In diagnosing and studying diseases, it is usually necessary to isolate and artificially
culture the pathogen in order to identify it properly. It is very useful to observe
microscopic preparations taken directly from diseased tissue or from an isolate.
Mounting preparations. Place the sample on a clean slide in a drop of mounting solution,
preferably sterile water or a dye for staining fungal structures to be observed in greater
contrast. Lactophenol, safranin and cotton blue are among the most commonly used
Preparations from diseased samples can be obtained in various ways depending on the
material: if the plant tissue has a cottony appearance or shows signs of pathogen
structures, take a sample by scraping the diseased tissue gently with a dissecting needle
or the tip of a razor blade (Figure 7 a). Carefully place the sample on the slide in a drop
of water or dye (Figure 7 b). Then place a coverslip gently with the help of a needle,
making sure that it covers the specimen completely without air bubbles (Figure 7c).
Use scotch tape for fast, non-permanent preparations of fungal growth in culture media.
This method is recommended for observing structures in their normal position and
growth stage (chains of spores, conidia or conidiophores). With the previously
described methods, the structures generally separate when they are touched with a
Figure 7 a, b, c. How to make a preparation for observation under the microscope.
Take a piece of scotch tape and lightly touch the sample or the culture on the Petri dish
or diseased tissue with the sticky side (Figure 8 a); then, place it on a drop of sterile
water on a slide (Figures 8 b, c).
When more detailed observations are needed (for example, of pathogen structures
within plant tissue), thin sectioning of the sample can be accomplished with a razor
blade or a scalpel. Gently hold leaves, stems, tubers, roots, etc., in position between
fingers for sectioning (Figure 9 a). Such sectioning of tissue samples will produce clean
cuts similar to those obtained with a microtome, an instrument designed for this
purpose that is generally not available because of its high cost. Sections should be
placed in a drop of mounting medium. Use a flat piece of wood or a longitudinal piece
of carrot for support when cutting soft, flexible plant tissues. With the tip of the sample
protruding, cut sections as thin as possible (Figure 9 b). Use this technique to produce
clear, complete sections of fungal structures such as pycnidia and perithecia, as well as
better and clearer images of naturally dark tissues.
Figure 8 a, b, c. Making a preparation using scotch tape.
- - - : : I I ~ ' : : " - - Razor blade
1--Razor blade
! Pith
Leaf wedged in notch
,....-__---'1..... -:;:::; Specimen in pith or carrot
- .
._ i
Figure 9 a and b. Making fine sections of fungal structures.
After placing the specimen in a drop of mounting medium, use a dissection needle to
put it in the desired position. Then use the needle to gently lower the coverslip onto the
slide, starting on one side, making sure it covers the specimen completely without air
bubbles, which can distort the image under the microscope. If necessary, softly press the
coverslip to force out excess solution and blot with filter paper or a paper towel.
To make semi-permanent preparations, flame the slide containing the sample for several
seconds until the drop of mounting medium boils (to eliminate bubbles); eliminate
excess medium outside the coverslip with filter paper.
Apply clear fingernail polish on the four sides of the coverslip to seal the sample.
Determining inoculum concentration
When evaluating germplasm for disease resistance or when doing specific studies on a
pathogen (epidemiology), it is often necessary to rely on artificial inoculation either in
the greenhouse or in the field. The appropriate inoculum concentration (number of
spores per milliliter) is determined depending on the host and pathogen under study.
The resulting infection should allow us to distinguish between resistant and susceptible
Concentration is determined with the help of a haemocytometer, with which spore
counts are made in fields of known dimensions. This provides the number of spores per
m1 of the initial suspension. Once the concentration of the stock suspension has been
determined, one can dilute the suspension as needed.
Procedure: Scrape plates with pure cultures of the fungus and suspend in a known
volume of distilled water. Stir the suspension to make it homogeneous, and filter it
through gauze or a coarse sieve to get rid of agar or other materials that may block the
nozzles during inoculation. Bring the filtrate to a known volume with distilled water.
Using a Pasteur pipette, place a drop in the middle of the haemocytometer chamber or
place a drop on each side, depending on the kind of haemocytometer you are using.
Then place the coverslip over the chamber making sure there are no air bubbles and that
the drop does not spill over the edges. Since the excess carries spores, this could
produce an erroneous count.
The haemocytometer has two counting fields, each of which is divided into nine large
squares; each square is subdivided into smaller squares (Figure 10). Since the sizes of
both squares are known, the number of spores/ml can be determined using specific
The counting field to be used is determined by spore size. If spores are large, it is easier
to use the four large comer squares (A, B, C, D) and the middle one (E) (Figure 10).
Spore counts are done at least six times, and then the average of the six counts is
1 2
For large spored fungi count
contents of A, B, C, D, E.
E 5 For small spored fungi count
contents of 1, 2. 3. 4. 5.
2, 5 ~ f r
= 3 4
C 0
F i g u ~ e 10. Haemocytometer diagram showing the counting fields (A, B, C, D, E).
Counting fields
Count number A B C D E Total
1 10* 15 12 13 11 61
2 18 15 10 20 13 76
3 25 15 18 16 14 88
4 12 14 15 18 13 72
5 15 13 17 14 11 70
6 15 13 12 18 20 78
*No. of conidia or propagules 445
Mean =74
With the resulting data, calculate the mean, which is multiplied by a constant factor
depending on the haemocytometer used. lhis will give the conidia concentration per ml.
74 x factor = Concentration in conidia/ml
This is the concentration of the initial suspension. To calculate a specific dilution, use
the following fonnula:
= Initial concentration (from spore counts)
VI = Initial volume (arbitrarily established when inoculum is prepared)
= Final desired concentration (depending on study)
= Final volume (unknown)
If the initial volume was 100 ml and a concentration of 30,000 conidia/ml is needed, then
estimated concentration x 100 ml
= ----------------- final volume (ml)
With the resulting data:
a) Estimate initial inoculum concentration.
b) Estimate the amount of liquid that should be added to the spore suspension to obtain
a concentration of 30,000 spores per ml.
Greenhouse inoculation
Artificial inoculation in the greenhouse has different purposes: to demonstrate Koch's
postulates, produce inoculum, do symptom characterization, select for genetic
resistance and conduct epidemiological studies. Inoculating under these conditions has
the following advantages: better control of the pathogen, better symptom evaluation,
ensures there is no interference from other organisms (as happens in the field), and the
inoculated material can be evaluated quickly. Generally, artificial inoculation in the
greenhouse is carried out on seedlings. However, other phenologic stages of the plant
can be used (depending on the pathogen under study).
The following inoculation exercise is very useful for selecting genetic material under
greenhouse conditions and can help to speed up the selection process in a breeding
program. Susceptible and resistant plants are used; they are inoculated with several
Helminthosporium species. In the case of Helminthosporium sativum, H. teres f. sp. teres, H.
teres f. sp. maculata and H. tritici-repentis, 10-12-day old seedlings are needed. Differences
among plants and resistance reactions can be evaluated 5-7 days after inoculation.
Seedlings to be inoculated can be prepared in several ways. The two methods described
in this exercise are similar, except at the beginning.
For the first method, use glassine bags with absorbent paper towels inside (Figure 11 a);
staple them together in the upper part, leaving enough space to introduce seeds to be
genninated. The bags containing seeds are placed in trays and supported by metal racks
(Figure 11 b). Water added to the trays will be absorbed by the paper towel inside the
glassine bags and reach the seed. This will allow seed gennination and supply water
needed later on. Always include susceptible and resistant controls.
In the second method, sow similar seed sets in paper cups filled with soil. As in the first
method, include susceptible and resistant controls.
From here onwards, both methods are the same. When seedlings are 10-12 days old,
scrape the pathogen cultured in Petri plates and dissolve in distilled water (if the
culture is on gram, shake with water), filter through a cheesecloth to eliminate any
pieces of agar and obtain as pure a conidial suspension as possible. Use the
haemacytomer to adjust the concentration to 30,000 conidia/ml; if Tween 20 is available,
add one drop to avoid aggregation of conidia and obtain a more homogeneous
concentration. Inoculate seedlings unifonnly using an atomizer (Figure 11 c). Separate
seedlings inoculated with H. sativum, H. teres and H. tritici-repentis. Identify the non-
inoculated controls and the susceptible and resistant ones.
Incubate the inoculated seedlings in a moist chamber for 2 h; then alternate 15 min
moisture/45 min light during 48 h for H. teres and H. tritici-repentis, and 18-24 h for H.
sativum. If a moist chamber is not available, similar results can be obtained by covering
the inoculated seedlings with plastic bags, and making sure moisture is available
continuously. Water the plants, spray the inside of the bags and seal them. The number
of hours they are to remain in the chamber should be detennined prior to the exercise
and adjusted to specific conditions. An electric humidifier is very useful, specially if
connected to a timer that provides moisture at intervals predetermined according to the
After 48 h (or 24, depending on the pathogen), remove seedlings from the chamber and
transfer to the greenhouse for 8-10 days. Observe symptoms and try to differentiate
lesions caused by H. sativum, H. teres f. sp. maculata and H. teres f. sp. teres from those
caused by H. tritici-repentis. Evaluate differences in susceptibility of the different
cultivars based on the scales given to you, using the susceptible and resistant controls as
references (Figure 11 d).
Do the following project as an exercise. Indicate how you would select germplasm in
the greenhouse or similar structure, with the facilities available in your country. For this.
project, choose a fungal disease that is economically important in the region where you
work; adjust the procedure to the conditions required by the pathogen.
a b
Figure 11 a, h, c, d. Trays adapted for growing and inoculating seedlings, and quickly
selecting them for resistance to pathogens that cause leaf blights.
Many species of Basidiomycetes are important parasites of cultivated plants, forest trees
and ornamentals. Some species of this class (for example, mushrooms) are grown for
human consumption; others are an important source of plant nutrients (mycorrhizal
fungi), and many are saprophytes.
Spores (basidiospores) of these fungi are produced outside a specialized structure called
a basidium, which may be septate (phragmobasidium) or non-septate (holobasidium).
Basidiospores are the result of plasmogamy (fusion of two protoplasts), karyogamy
(fusion of two nuclei) and meiosis.
The rusts
The rust fungi are a large, economically important group of plant pathogens. They attack
most plant species, but on cereal crops they have been the focus of much attention for a
long period of human history because of their high incidence and the severe damage
they cause on those crops. The life cycle of cereal rusts typically includes sexual and
asexual phases and as many as five different spore stages.
Wheat is attacked by stem rust caused by Puccina graminis f. sp. tritici, stripe (yellow)
rust (Puccinia striiformis f. sp. tritici), and leaf rust (Puccinia recondita f. sp. tritici). Stem
rust is more prevalent in warm climates, whereas stripe rust is favored in cooler areas.
An intermediate climate favors leaf rust, and today it is the most Widespread and
damaging of the three diseases.
Stem rust produces elongated, reddish brown pustules on the stems, sheaths and necks
of the plants. Leaf rust lesions are slightly lighter (orange-brown), smaller and oval
shaped, and most evident on leaf blades. Stripe rust is even lighter (yellow to orange-
yellow) and occurs in a linear arrangement on various foliar parts and the glumes.
Development of effective control measures for wheat rusts started early in this century when
it was discovered that resistance existed and was often inherited through a single gene. The
capacity of a pathogen strain to overcome a specific gene for resistance is often conditioned
by a single gene as well, and this host-parasite relation is called the 'gene-for-gene' concept.
As resistant cultivars were grown for years over large areas, pathogen strains appeared
to which resistance was not effective. Strains that differ in their ability (virulence) to
attack a cultivar or group of cultivars are called (physiologic) races. A race is defined as a
different avirulence pattern observed among a group of pathogen cultures or isolates
when tested on a set of selected host cultivars or lines.
For example, about 40 different major genes for leaf rust resistance have been
discovered in wheat; however, isolates of the fungus possessing virulence for many of
these genes have also been found. Since there are two descriptive classes (avirulence
and virulence) of the pathogen possible for each of the 40 known host resistance genes,
the possible number of races (Le. different combinations of virulence/ avirulence genes)
is 240, or more than 34 billion. This gives us an idea of these pathogens' great variability.
Single-gene resistance and the occurrence of races are also found with other fungi (for
example, mildews and potato late blight).
Monitoring the leaf rust population
For the above reasons, it is important to monitor races of the pathogen, and to test new
cultivars against them when breeding for resistance. This can give early warning that a
race or virulence combination may be building up, and provide information useful in
developing strategies for using resistance (for example, the release of cultivars).
Following are instructions on how to monitor a leaf rust population and determine its
race composition. The objectives of this exercise are to: 1) become acquainted with leaf
rust of wheat, and evaluate reactions of susceptibility and resistance in wheat; 2)
illustrate the interaction of rust isolates with different wheat lines, and demonstrate the
presence of races; and 3) provide techniques for the practical monitoring of virulence in
a leaf rust population.
For this exercise, it is best to use seed of near-isogenic (or differential) lines of spring
wheat cultivar Thatcher. Each line possesses a different single gene for resistance bred
into spring wheat cultivar Thatcher through a process known as backcrossing. The
genetic constitution of these 'isolines' is similar, except for their specific resistance gene.
Isolines for all known genes or only for selected genes can be used for this exercise.
Spores of at least two isolates of the leaf rust fungus are needed to show a differential
response. Each isolate is the progeny of a single rust pustule.
1. Plant isolines as clumps (6-8 seeds each) in a tray starting from the front left corner
(label the spot) and moving to the right. Keep in a greenhouse at 18-24C until the
first leaf is fully extended (about 1 week). Seedlings must be kept isolated from any
rust-infected plants. Water and fertilize as needed.
2. Inoculate each set of isolines with a different isolate of the fungus as follows:
suspend spores in mineral oil or water, and spray or rub onto the leaf surfaces. Be
careful not to mix spores of different isolates; wash your hands and, if using a
sprayer, rinse with 70% ethanol before inoculating the second set of isolines with
another isolate of the fungus. Allow the seedlings to dry for about 30 min after
3. Spores require free moisture on the leaf surface for germination and penetration. In
nature this is provided by overnight dew. To provide the needed moisture, spray
plants with fine water mist and incubate overnight in a closed moist chamber. The
next day, open the chamber partially and allow plants to dry off slowly. After 1 h,
transfer them to a greenhouse bench and maintain at 16-24C. The period of host
tissue colonization between penetration and sporulation is called the latent period.
The length of the latent period can be determined by noting when the first rust
pustules break the epidermis and release urediniospores. Pustule development takes
about 10-14 days.
4. After two weeks, observe uredinia under a dissecting microscope. Rust fungi are
'biotrophs' since they are obligate parasites (they need a living host). Infection leads
to a physical association in which haustoria (feeding structures) invade living cells
to obtain nutrients but do not immediately destroy them. Infections are usually local
and the damage to the host results from the presence of many infections. Plants are
weakened because nutrients and water are redirected toward the growth and
reproduction of the fungus. Invaded cells remain alive and active until the parasite
reproduces by developing spores.
5. Use the table on p. 28 to record disease r e a ~ t i o n for each host isoline/pathogen
isolate combination. Reactions may range from highly susceptible (large sporulating
pustules) to highly resistant (tiny chlorotic flecks only), with intermediate levels
(Figure 12 a, b, c). More precise evaluations may be made using a subjective visual
scale of 0-4 or 0-9,0 being the most resistant. For race identification, reactions are of
two types: high (susceptible host/virulent pathogen) and low (resistant host/
avirulent pathogen). Intermediate reactions may be difficult to rate, but are
considered resistant (low), since any reduction in spore production, chlorosis or
necrosis implies less disease development and reduces the rate of disease buildup.
Rust races are sequentially designated using code numbers and a dichotomous key or
an avirulence/virulence formula. The code or race number relates only to the set or host
group used. An earlier standard wheat set used for race identification was discarded
following the development of isolines. No new standard set has been developed or
widely used. At present, an avirulence/virulence formula is used to characterize each
rust culture. An example would be Lr I, 9, 16, 24, 26 /2a, 2c, and 3, which indicates that
isolines Lr 1,9, 16,24, and 26 are resistant and isolines Lr 2a, 2c, and 3 are susceptible to
this rust isolate. Conversely, the isolate is avirulent to isolines Lr 1,9, 16,24, and 26 and
virulent to isolines Lr 2a, 2c, and 3. It represents a race different from a culture that is
determined to be Lr 2a, 2c, 9, 24, 26/1, 3, 16.
RA Mcintosh
o 1 2 3 4 x
a. Stem rust (Puccina graminis f. sp. tritici)
R.P. Singh
o 1 2 3 4 x
I. Leaf rust (Puccinia recondita f. sp. tritici)
c. Stripe rust (Puccini a striiformis f. sp. tritici)
Figure 12. Evaluation scales for rusts on wheat seedlings under greenhouse conditions.
Reactions of eight wheat isolines to two leaf rust isolates.
Wheat isoline
Lr1 Lr2a Lr2c Lr3 Lr9 Lr16 Lr24 Lr26
Rust isolate A
Rust isolate B
1. How did the two fungal cultures differ from each other on each wheat isoline?
2. How did the wheat isolines differ from each other in this test?
3. If you were recommending sources of resistance to a wheat breeder, which of these
genes would you recommend? Would you need additional information to make a
useful recommendation? Explain.
4. Would any of these genes by itself be useful to a wheat breeder?
5. Would genetic recombinations of these resistances be useful?
6. Why is national or regional rust race monitoring useful to a wheat breeder working
on developing resistant cultivars?
7. Besides wheat breeding, can you think of other areas where the information from a
large scale rust race survey might be useful?
Agrios, G.N. 1978. Plant Pathology (second ed.). Academic Press, Orlando, FL. 703 pp.
(Chapter 6, Genetics and plant disease).
Hanson, C.H., Schafer, J.F., and Turnipseed, S.G. 1979. Genetic resistance for crop
protection. Chapter 3.2 in: Introduction to Crop Protection. W.B. Ennis, Jr., ed.
American Society of Agronomy. Madison, WI. 524 pp.
Kenaga, c.B. 1974. Principles of Phytopathology (second ed.). Waveland Press, Prospect
Heights, IL. 402 pp. (Chapter 18, Disease control-breeding for resistance).
Wiese, M.V. 1987. Compendium of Wheat Diseases (second ed.). American
Phytopathological Society, ST. Paul, MN. pp. 37-42.
Smuts and bunts
Several genera of the class Basidiomycetes are included under the general names of
smuts and bunts. Smuts and bunts are obligate pathogens that can remain dormant in
the soil for long periods of time. This group of fungi is widely known because the
symptoms they produce are very easy to recognize: they sporulate (produce brown or
black spores) primarily in the grain, inflorescence, leaves, and stems. They attack cereals
(wheat, barley, oats, maize, rice, etc.) and other economically important crops (potato,
sugar cane, onion, etc.).
One of their most important taxonomic characteristics is that teliospores are produced
individually, in pairs or in groups. Also important are teliospore size, color, and
morphology; the presence and location of sterile cells; the sporulation site and the host.
In contrast to the rusts, fertilization takes place through the joining of the fungi's
compatible propagules. Smuts and bunts that affect wheat are TiIletia caries and T.
foetida, causal agents of common bunt; TiIletia controversa, causal agent of dwarf bunt;
Tilletia indica, causal agent of Karnal bunt; Ustilago tritici, causal agent of loose smut; and
Urocystis agropyri, causal agent of flag smut.
Identifying loose smut and Karnal bunt
The following is a description of how to do a germination test on teliospores (spores) to
identify the smuts and bunts.
Loose smut. Take infected spike samples, put them in a container with water + Tween 20
or another surfactant, and shake. Use one drop of Tween per liter of water, and shake
gently until it dilutes. Strain the spore suspension through a 60 IJ,m mesh or smaller to
retain large particles (teliospores measure 5-9 IJ,m in diameter). Centrifuge at 3000 rpm
to concentrate teliospores at the base of the test tube and discard the supernatant.
Prepare a sodium hypochlorite and water (1:9, v:v) solution. Add the solution to the test
tube containing teliospores for surface sterilization, shake, centrifuge, and discard the
supernatant. Add sterile water to the test tube to remove the sodium hypochlorite,
shake, centrifuge, and discard the supernatant; add more sterile water and repeat once
Using a sterile syringe or a pipette, transfer teliospores to a Petri plate containing 1.5-2%
agar (15-20 g agar per liter of water). Incubate plates at laboratory temperature (18-
22C). Seven days later, examine the plates and take notes on teliospore germination.
'.:. 0.
Karnal bunt. In the case of Tilletia indica, take infected grains and follow the same
method described for Ustilago tritici. To obtain better germination, teliospores are kept
in the water-Tween solution for 24 h before surface sterilizing with sodium
hypochlorite. A 60-lJ,m mesh is used to strain the solution because teliospores measure
22-49 IJ,m in diameter.
Inoculation methods
There are several inoculation methods, but only one for loose smut and one for Karnal
bunt are de!;lcribed here. ' .
Loose smut: Dusting. Choose spikes at the flowering-anthesis stage and prepare them as
for emasculation (cutting awns along with parts of the glumes, lemma, and palea).
Cover them with glassine bags and dust with teliospores over the top (cut bag top with
scissors and close with clips after dusting).
Kamal bunt: Boot inoculation. Colonies derived from germinated teliospores are
transferred to a nutrient-rich medium (like PDA) for multiplication. Use the following
process: Check that there is no contamination on plates containing germinating
teliospores. Cut small pieces of agar containing germinating teliospores using a sterile
(by flaming) spatula and transfer them to Petri plates containing PDA; cover the plates,
tum them over (the fungus will sporulate downwards), and wait 4-6 days for colonies
to develop. Add sterile water and scrape with a sterile spatula; inoculate more PDA
plates using a sterile syringe or a pipette, then wait 5-7 days for the fungus to cover the
medium completely.
After that time, add water, scrape, and strain through cheesecloth (to remove any agar
or hyphae aggregates that might clog the needles during inoculation). After scraping
about 15 plates, calculate the initial propagule concentration per milliliter using a
haemocytometer and add the necessary water (10,000/ ml). During inoculation inject 1
ml of that concentration into the boot.
a b c
Figure 13 a. Fungal cultures and cuts on PDA. b. Inverted colony cuts initiating
growth. c. Inoculum development and multiplication.
The Ascomycetes comprise several thousand species that can be classified as being
anywhere from strictly saprophytic to obligate parasites of higher plants. There are
obligate parasites that attack and can severely damage small grain cereals.
The life cycle of the Ascomycetes has two phases: the asexual and sexual. During the
first, the fungus gives rise to conidiophores, which are structures that generate asexual
spores and conidia. Conidiophores can be born individually or in groups, directly from
the host or in fruiting bodies known as pycnidia or acervuli. From the
phytopathological point of view, this phase is very important because it is repeated
during the crop cycle, and conidia can infect leaves, stems, spikes, as well as grains.
The fusion of two compatible nuclei takes place during the second phase, and as a
result, fruiting bodies (perithecia, cleistothecia or apothecia) are formed. Fruiting bodies
can withstand unfavorable humidity and temperature conditions in the absence of a
host. Asci are produced in these fruiting bodies and become active at the beginning of a
new crop cycle. This is the overwintering stage, although most asci and ascospores are
not formed or do not mature until late winter or early spring. Therefore, the fungus can
also overwinter as mycelium and sometimes as conidia.
The mycelium of the Ascomycetes is made up of well-developed, thick or thin hyphae,
profusely branched and divided by simple septa. Pathogens in this group of fungi
induce important cereal diseases such as foliar blights caused by Helminthosporium and
Septoria spp.
Identification of spot blotch
caused by Helminthosporium sativum
Spot blotch caused by H. sativum appears from the onset of foliage development, and
multiplies primarily on leaves after heading. Since the fungus can attack the crown,
roots, node, leaf sheaths, ears and kernels, it is considered an important pathogen
especially in the subtropics, where optimum environmental conditions (high
temperature and high humidity) are found.
This fungus produces its asexual reproductive structures consisting of conidia-bearing
conidiophores on leaves and other parts of the plant. The isolation of H. sativum is
simple, because in general it grows readily on PDA, or even in just a moist chamber.
The sexual phase is not frequently found in nature, and has only been described under
the agroecological conditions of Zambia.
Symptoms and isolation of the fungus
Place a sample on the diagnostic sheet and describe the symptoms you see. Prepare 1%
sodium hypochlorite (1 ml sodium hypochlorite in 99 ml sterile distilled water; if
available, add one drop of Tween 20 to reduce surface tension). Pour the solution and
the sterile distilled water into separate Petri plates. Cut small pieces of leaves showing
incipient lesions and place them in hypochlorite for 1 minute. Dip the tip of the forceps
in alcohol and flame it over a burner for a few seconds. With the forceps transfer leaf
pieces to sterile water and rinse off the excess hypochlorite; allow them to dry on sterile
filter paper. Under sterile conditions (in a microvoid and/ or an area disinfected with
alcohol or hypochlorite), plate the pieces in an orderly fashion on PDA (5-7 pieces per
At the same time, incubate a sample in a moist chamber for 3-7 days. Make sure that the
filter paper is always wet, adding water if necessary. After this period, there should be
substantial fungal growth. Describe characteristics of the colonies. Take a tiny portion of
the fungal growth and prepare a temporary motmt in water; observe tmder the
compotmd microscope using the objective with the lowest magnification. For fine
details, use higher magnification. Draw and describe the structures observed:
mycelium, conidiophores, conidia, etc. Search in the literature to compare the conditions
that favor fungal attacks on roots and on leaves.
Identification of tan spot
caused by Helminthosporium tritici-repentis
Tan spot (also known as leaf blight or eye spot), caused by Helminthosporium tritici-
repentis, is a disease that attacks wheat, triticale and some grasses. Symptoms appear as
necrotic lesions with a chlorotic halo that vary in size depending on disease severity;
lesions may coalesce and destroy the whole leaf. An important diagnostic feature is a
dark spot in the middle of the lesion. This feature is not exclusive of tan spot, however,
as it also occurs on lesions caused by H. sativum and Septoria nodorum. For this reason, a
final diagnosis can only be made by observing ftmgal structures under the compotmd
The causal agent does not grow or sporulate easily on culture media because it often
initiates the formation of sexual structures (pseudothecia), although they do not mature.
Nevertheless, it has been observed that if 5-7 day-old colonies are covered with sterile
water and scraped, sporulation is induced within 48 h.
The sexual phase has been reported in many parts of the world. Formation of sexual
structures seems to depend on environmental conditions during winter and early
spring. They are generally fotmd on crop residues left in the field after harvest.
Symptoms and isolation of the fungus
Select leaves showing typical lesions for your diagnostic sheet and describe symptoms.
Cut small pieces of leaf containing incipient lesions; surface disinfect them in 1%
sodium hypochlorite during 1-2 min. Rinse in sterile water and let them dry on sterile
filter paper. Put five pieces per Petri plate on 30% V-8 medium (very efficient for
isolating and producing spores of this fungus).
Incubate plates at 20-22C under near ultraviolet fluorescent lights for 5-7 days using a
10 h-14 h light-darkness regime (essential for sporulation). To stimulate conidia
production, add sterile water and scrape the surface of 5-6 day-old colonies with a
sterile spatula. Remove inoculum and continue incubation of the plates for an
additional 48 h. Past this time, make preparations and observe under the compound
microscope. Describe colony characteristics. Describe and draw the structures observed.
Identification of Helminthosporium spp.,
causal agents of barley net and spot blotch
Barley net blotch caused by Helminthosporium teres f. sp. teres is common in cold, humid
areas wherever barley is grown. A dark spot develops into a net-like pattern having
transversal and longitudinal bands. It usually occurs on leaves, although on very
susceptible cultivars it may attack the spike and reach the kernels.
Helminthosporium teres f. sp. maculata and/ or H. sativum can cause another blotch that
produces symptoms very similar to those caused by H. sativum. These two pathogens
can be differentiated by observing their conidia under the microscope.
Helminthosporium teres f. sp. teres and H. teres f. sp. maculata show the same
morphological development on artificial media; however, they are capable of inducing
completely different symptoms. The sexual phase is often found in crop residues during
the winter cycle.
Symptoms and isolation of the fungus
Collect a sample of each disease for the diagnostic sheet, and describe their respective
symptoms. Cut small pieces of diseased tissue from each sample, surface sterilize them
in 3% sodium hypochlorite for 1 min, and rinse in sterile water. Dry them on sterile
filter paper and plate five pieces from each sample on V-8 medium (15%). Incubate at
20-22C for 5-7 days under alternating periods of light and darkness; H. teres will not
sporulate if those conditions are not met. Observe samples under the microscope, and
describe the shape and color of colonies. Draw the observed structures, and differentiate
conidia of the various Helminthosporium species by shape and size.
Identification of leaf blotch caused by
Mycosphaerella graminicola (Septoria tritici)
and glume blotch caused by
Lepthosphaeria nodorum (Septoria nodorum)
Wheat is attacked by several species of the genus Septoria. Among the most important
are S. tritici and S. nodorum. The first, causal agent of leaf blotch, occurs in regions with
high rainfall and high relative humidity, and temperatures between 18 and 24C. This
blotch is identified by the presence of black asexual bodies (pycnidia) formed by the
fungus, which extend from both sides of the leaf epidermis and are distributed in
parallel lines. Inside the pycnidia there are long, thin pycnidiospores, which, when
mature, come out of the pycnidia through an ostiole (pycnidial aperture) if favorable
moist conditions occur.
Septoria nodorum is present in almost the same conditions as S. tritici, but needs more
temperate conditions. In wheat, it may attack all plant parts above the ground,
particularly the glumes, nodes, internodes and leaves. In contrast to S. tritici, S. nodorum
pycnidia are black to pinkish in color and immersed in the epidermal tissue at random.
Pycnidiospores are small, cylindrical and transparent, with 0-3 septa.
Although in both cases the sexual phase often occurs at the end of the crop cycle,
identification is difficult because pycnidia are similar to perithecia. Proper identification
can be only done using special laboratory techniques. Both species may be isolated and
cultivated on specific artificial media.
Symptoms and isolation of the fungus
Collect a sample of each disease for the diagnostic sheet, and describe the symptoms.
Attach diseased leaf segments to a glass slide with the pycnidia facing up. Place the
slide in a Petri dish with filter paper saturated with sterile water to make a moist
chamber; seal the plates and place them under the light at a distance of 15-20 em. One or
two hours later, observe the Petri dish (with its cover still on), under the stereoscope;
there should be exudates oozing through the pycnidial ostiole. Septoria tritici exudate is
grayish white, while S. nodorum exudate is pinkish. With a sterile toothpick, near a
burner, take a drop of exudate and put it on the plate containing the specific medium.
Incubate the plate for 6-8 days. Describe colony characteristics.
Cut fine pycnidial pieces, make slide preparations and observe them under the
microscope; describe and draw the type of pycnidiospore produced by each species.
Identification of head scab of
wheat caused by Fusarium spp.
Head scab of wheat is a disease that appears when heading starts, although the
flowering stage is the most susceptible. In Mexico, Fusarium graminearum is the most
common species, although F. culmorum, F. nivale, F. equiseti and F. avenaceum are also
Identifying Fusarium spp. is not easy because their differences are not conspicuous.
Although PDA works well when used for isolation and identification, there are other
specific media for isolating this genus, such as com meal agar, which is commercially
available, and PCNB. These media are useful for inducing sporulation and for isolation,
and problems with saprophytes can be avoided. Criteria used for identifying Fusarium
species are the presence and shape of microconidia, macroconidia and chlamydospores
(for more details, see 'Symptoms and isolation of Fusarium' on p. 40). The most
commonly used taxonomic keys are those of Booth and Toussoun and Nelson
(references in the same section).
Spikes affected by the pathogen show different colors ranging from pinkish- white to
orange. The sexual phase develops on the glumes at the end of the crop cycle in some
areas and overwinters on crop residues.
Symptoms and isolation of the fungus
Attach an infected spike onto the diagnostic sheet and describe disease symptoms. Use
sterile forceps to carefully separate floral structures and take kernels from infected
spikelets, especially those showing mycelium, and directly inoculate PDA plates.
Incubate plates for 5-7 days under near ultraviolet light (to stimulate development of
the asexual phase). At the end of this period, observe samples under the microscope and
try to identify the species. If there is contamination, try to purify the culture by taking a
small piece from the edge of the desired colony, transferring it to another PDA plate and
incubating for 5-7 days.
To obtain 100% pure cultures, use a conidial suspension to make serial dilutions on
water-agar. Within 12 hours, isolate individual germinating conidia with a dissecting
needle. Describe colony characteristics. Draw and describe the structures seen under the
Inoculum preparation and field inoculation
There are two main methods used for evaluating germplasm for scab resistance:
inoculation of individual spikes or bulk inoculation.
Scrape fungal propagules from several plates containing pure cultures of the fungus as
follows: add sterile distilled water to the plates and scrape with a spatula or a scalpel.
Strain the suspension through cheesecloth and use the haemocytometer to adjust to a
concentration of 50,000 spores per ml. If possible, prepare inoculum just before
inoculating; however, inoculum remains infectious for up to 36 h if maintained at 4-5C.
Inoculation of individual spikes (cotton method). Select and label 10 spikes per line. Anthers
should be just starting to emerge from florets. Cut the awns to facilitate bagging. Soak a
small piece of cotton in the spore suspension; open the glumes and inoculate the middle
portion of the spike by placing a tiny portion of the soaked cotton on each side. Cover
with a glassine bag.
Bulk inoculation. To evaluate large numbers of advanced lines or segregating
populations, spray the inoculum from a distance of 10-15 em, until spikes are covered
uniformly. Inoculations should be carried out at least three times a week if
environmental conditions are less than optimal. Inoculation should be done when 5-
10% of anthers in the plot have emerged.
Inoculated materials are evaluated 30-40 days after inoculation, at the end of
grainfilling. At this stage spikes are still green and there is a strong contrast between the
color of healthy spikes (green) and infected spikes (yellow). Evaluation can be done as a
percentage, based on the number of infected spikes compared to the total number of
There are many fungi in nature which, despite producing septate mycelia, rarely
reproduce sexually. For this reason, they are termed Imperfect Fungi or
Deuteromycetes. Most are either saprobes or weak parasites of plants, animals and man.
Some are parasitic on other fungi and nematodes.
Deuteromycetes survive perfectly well in nature without sexual reproduction. Asexual
reproduction is initiated from a stroma that generates conidia, from conidia that
develop without special hyphae (conidiophores), or from fruiting bodies such as
pycnidia, acervuli, sporodochia and synnemata.
Identification of black point
caused by Alternaria alternata,
A. triticina, and/or Helminthosporium sativum
Black point, a blackening of the embryo end of the seed, may be induced by any of three
species: Alternaria alternata, A. triticina, and/ or Helminthosporium sativum. Identifying
which of the three is the cause of the damage requires isolating a sample on a culture
medium and observing it under the microscope.
Symptoms and isolation of the pathogen
Collect a diseased sample for the diagnostic sheet and describe symptoms. Place 3%
sodium hypochlorite and sterile water in separate Petri plates; sterilize kernels by
placing in sodium hypochlorite for 1 min. With sterile forceps transfer kernels to the
sterile water to rinse off excess hypochlorite. Dry off excess water on a paper towel to
reduce the possibility of contaminant bacteria. Then place five kernels from Cd.
Obregon and five from Poza Rica on different PDA plates.
Incubate the plates for 5-7 days, make slide preparations and observe under the
microscope. Describe the color and shape of each colony. Draw the structures observed
on each isolate. Describe the shape, number of septa and other conidial characteristics
observed on each isolate. Search the literature for the conditions that favor damage by
each of the different pathogens.
Identification of Rhynchosporium secalis,
causal agent of barley scald
Scald (causal agent: Rhynchosporium secalis) is one of the most important diseases of
barley in cold and humid areas, as well as in tropical highlands where there is high
rainfall and temperatures are low because of the altitude. This disease primarily affects
the leaves, but it can also affect the glumes, awns and grains. Symptoms in the field are
easily recognized because they start as oval, elongated or elliptical lesions, with dark-
brown or reddish edges, and gray or yellowish-brown centers.
Isolation and culture of the fungus are somewhat difficult. Due to its slow growth rate,
the first signs of growth appear after 14 days of incubation. Therefore, any growth
appearing before then should be eliminated because it is probably a contaminant. For
quick identification, make direct preparations from diseased tissue showing conidia and
observe under the microscope. However, if the objective is to isolate in order to collect
virulences for testing barley genotypes for resistance, the following method is
Symptoms and isolation of the pathogen
Collect barley leaves with scald symptoms for the diagnostic sheet and describe the
symptoms observed.
Direct identification of diseased tissue. With a razor blade or scalpel, scrape the leaf surface
of clear lesions, and make a preparation. Observe the specimen under the microscope;
draw and describe the fungal structures.
Isolation on lima bean agar (LBA) and multiplication. Cut small pieces of diseased tissue
showing young lesions, preferably grayish-green lesions with no necrotic margins. Dip
in 70% ethyl alcohol for 15-20 seconds and transfer to sodium hypochlorite (commercial
grade, 5.25% in weight) diluted in water (1:9). Soak (making sure tissues are completely
submerged) in the hypochlorite for 90 seconds. (Soaking time is important: if samples
are soaked for only 60 seconds, they will show a lot of contamination in the fungal
cultures; if samples are soaked for two minutes or longer, the fungus will be
eliminated.) Transfer the pieces of tissue to Petri plates containing LBA.
Components of LBA medium:
Commercial LBA 23g
(8 g lima bean infusion,
15 g agar)
Pure agar 5g
Distilled water 1000 ml
Add 5 g pure agar to the commercial LBA; mix with distilled water.
Incubate Petri plates at 18-20C. Schein and Kerelo (1956) indicate that growth can be
observed after 5-7 days' incubation. However, in our experience 10-14 days are
required. Growth of the fungus on LBA is slow, but the small colonies produced are
pure. To obtain a large number of spores per culture, use the zigzag culture technique to
inoculate tubes or Petri plates as follows.
Pick up the incipient growth with a sterile needle and dilute in 1 ml sterile water; shake
vigorously to obtain a homogeneous suspension. Take a small amount with a
previously flamed and cooled Pasteur pipette and deposit it on the culture medium.
Bend the tip of the pipette with the flame, let it cool, then use it to distribute the
inoculum smoothly and as uniformly as possible on the culture medium. After eight
days, the culture will have a yeast-like appearance and contain 30 million spores or
more. All colonies obtained on this medium are pink, which contrasts with the black or
brown color of colonies on other culture media.
Schein R.D., and J.W. Kerelo. 1956. Culturing Rhynchosporium secalis. Plant Disease
Reporter 4(9):814-815.
Soil pathogens produce diseases that inhibit development of the plant's root system
and/or destroy it. It is difficult to identify all the potential problems soil pathogens can
cause; however, it is possible to group them according to the climatic zones where they
are prevalent. Thus, Helminthosporium, Fusarium, and Pythium are important in cool
climates, Sclerotium rolfsii in subtropical regions, and Gaeumannomyces graminis in cold,
rainy areas.
In general these fungi cause such symptoms as poor plant growth, fewer tillers, and
early maturity (white heads). Also, patches of diseased plants can be observed in the
Symptoms caused by Fusarium
and Helminthosporium
Fusarium and Helminthosporium can be found in many places due to their wide host
range and temperature adaptation. Both fungi interfere with plant establishment and
pre- and post-emergence of the roots, particularly if soil temperature is high (25-30C) at
planting. Moist soils are more conducive to Helminthosporium damage, while dry soils
favor Fusarium, especially when plants reach maturity under water stress.
When the wheat crop reaches maturity, white heads occur randomly or in irregular
patches in the field. If subcrown internodes of plants with white heads are light to dark
brown, it is a sign of Fusarium infection. The development of white heads is closely
related to drought stress in cool climates; if drought stress increases during plant
maturity, it is likely that white heads will be observed in areas where the pathogen is
The most characteristic symptoms of Helminthosporium are brown to black lesions on the
internode below the crown, which become more severe as plants grow. As long as the
subcrowns remain intact, changes in severity can be observed during the growth cycle.
Helminthosporium can also cause white head symptoms when plants reach maturity, just
as Fusarium and Gaeumannomyces (take-all) do.
Symptoms and isolation of Fusarium
PDA can be used as a general culture medium for isolating Fusarium, but certain types
of studies require selective media. The preparation of Fusarium selective medium for
about 40-50 Petri plates (15 X 100 mm) is as follows:
Deionized water 1000 ml
Agar 20.0 g
Peptone 15.0 g
Monobasic potassium phosphate (KH
) 1.0 g
Magnesium sulfate (MgS0
0) 0.5 g
Mix, dissolve, and sterilize. Cool medium to 45-50C, then add:
PCNB (pentachlorobenzene; Terraclor) 0.5 g
Bacto-oxgall 1.0 g
Streptomycin sulfate 0.1 g
Chlorotetracycline-HCL 0.05 g
Streptomycin sulfate is dissolved in 3-5 ml of 95% ethyl alcohol; the other ingredients
are added dry. The medium should be shaken gently for 2-3 minutes, taking care not to
let bubbles form.
Procedure: Select tissues of plants collected in the field to make isolates. Observe the
discolored tissue under the stereoscope. Sometimes it is possible to see mycelium
growing on and in the tissue of the first internode. In this case, tissue should not be
surface sterilized.
Remove leaf sheaths with forceps as aseptically as possible (do not touch tissue with
your fingers). Flame scissors, then cut the internode into small segments (0.5 cm or
smaller) and place 5-10 pieces in a Petri plate, either on PDA or the selective medium.
After a 3-5 day incubation period, check development of Fusarium. A pure white to
reddish colony with a yellow shadow can be observed, and the mycelial growth is aerial
and hairy. Purify the subcultures at this stage and place on the same culture medium.
Examine the subcultures under the microscope to determine if they are pure, so that
they can be used for further identification and storage.
To identify Fusarium species, it is necessary to work with cultures derived from single
conidia. However, in studies dealing with plant resistance, a mixture of cultures should
be used to maintain broad genetic diversity in the inoculum. Identification work is done
in the laboratory using preViously isolated and purified cultures that have not been
derived from a single spore (i.e., non monosporic). Host resistance should never be
evaluated using only isolates derived from single conidia.
CMA and PDA are the media of choice for this work, as well as for initiating cultures of
specimens kept in storage. Pieces of these cultures can be used to infect wheat-seed
medium for pathogenicity tests or to increase inoculum for field tests.
To identify Fusarium species, isolates should be made to sporulate under standard
conditions using one culture medium. Tousson and Nelson recommend immersing
carnation leaf pieces in water, then placing 4-5 pieces on the surface of 2% water agar at
points equidistant from the center, where a piece of the growing fungal culture is
placed. Repeat the procedure on several plates. The plates are sealed and incubated at
room temperature (25C) using alternating cycles of 12 h fluorescent light/12 h
After 6-7 days, the plates should be examined for sporulation. Once sporulation has
started, observations and notes should be taken about the presence of microconidia,
macroconidia, chlamydospores, etc. Based on the morphology of the observed
structures and using the Fusarium taxonomic keys, start reducing the number of species
that could be present. The following characteristics are important for using these keys
a) Septate mycelium.
b) Macroconidia: They are large and have more than two septa. Observe the apical cell,
basal cell (foot cell) and number of septa. The shape of the apical and basal cells is
important. How macroconidia are borne on the conidiophore may also be important.
c) Microconidia: They are small with 1-2 cells. Not all Fusarium species produce
microconidia, so their presence or absence is important.
d) Chlamydospores: They are latent, thick-walled spores produced by hyphae and
conidia. Their presence or absence is important. Generally, they are produced by
cultures more than a week old.
The examination process should be slowly and carefully done. Select 1-4 isolates
representative of different type colonies (i.e., white or multi-colored colonies). Look for
macroconidia and examine them, and determine the presence or absence of
microconidia. Once you have become familiar with the species you are studying, it will
be easier to classify the rest of the isolates.
Booth, C. 1977. Fusarium. Laboratory Guide to the Identification of the Major Species.
Commonwealth Mycological Institute. Kew, Surrey England. 58 pp.
Booth, C. 1977. The Genus Fusarium. Commonwealth Mycological Institute. Kew,
Surrey, England. 237 pp.
Burgess, L.W., C.M. Liddell, and B.A. Summerell. 1988. Laboratory manual for
Fusarium research. 2nd. edition. Fusarium Research Laboratory Department of
Plant Pathology and Australia Entomology. The University of Sydney.
Francis, R.G., and L.W. Burges. 1977. Characteristics of two populations of Fusarium
roseum 'graminearum' in Eastern Australia. Trans. Br. Mycol. Soc. 68:421-427.
Nelson, P.E., T.A. Tousson, and W.EO. Marasas. 1983. Fusarium species. University Park
and London: The Pennsylvania State University Press. 193 pp.
Tousson, T.A., and P.E. Nelson. 1976. Fusarium. A pictorial guide to the identification of
Fusarium species according to the taxonomic system of Synder and Hansen. 2nd.
ed. University Park and London: The Pennsylvania State University Press. 43 pp.
Zillinsky, EJ. 1984. Common Diseases of Small Grain Cereals: A guide to identification.
Mexico D.E: CIMMYT. 141 pp.
Isolation and identification of Helminthosporium
In general, it is easier to isolate Helminthosporium than Fusarium. PDA can be used for
general purposes, but selective media such as Czapek's modified broth should be the
medium of choice for specific studies.
Deionized water 1000 ml
Czapek-Dox broth 35 g
Agar 15 g
After mixing and sterilizing the medium, let it cool to 46-50C and then add:
Streptomycin sulfate 0.1 g
Benomyl (Benlate 50 WP) 0.004 to 0.008 g
Czapek's broth:
Sodium nitrate (NaN0
Dibasic potassium phosphate (K
Magnesium sulfate (MgS0
Potassium chloride (KCI)
Ferrous sulfate (FeS0
Distilled water
30.0 g
3.0 g
1.0 g
0.5 g
0.5 g
0.01 g
1000 ml
Growth of H. sativum is usually visible as a white micelial front that moves forward,
leaving a dark area. To confirm identification, cultures must be microscopically
examined because Alternaria spp. show similar growth characteristics on the medium,
although their conidia are clearly different and produced in chains.
Helminthosporium spiciferum can also be isolated by this method; its growth, of a dark-
hairy discolored type, is quite distinctive. Helminthosporium spiciferum produces conidia
on verticils at the apex of the conidiophores. Conidia are much smaller than those of H.
sativum, which are produced individually. With some experience, it is easy to detect
these differences with the aid of a stereoscope.
Procedure: To isolate fungi from plant tissue or the internodes below the crown, use the
following procedure:
Wash all plant material before bringing it into the laboratory. Cut the internodes below
the crown and the seminal roots. Surface disinfect samples with a 1:1 ethyl alcohol:5%
sodium hypochlorite solution for 1 min. Rinse in sterile water twice and dry on paper
towels. Plate five pieces in the medium and incubate at 22C for five days.
Luttrell, E.S. 1964. Systematics of Helminthosporium and related genera. Mycologia
Shoemaker, R.A. 1959. Nomenclature of Drechslera and Bipolaris, grass parasites
segregated for 'Helminthosporium'. Can. J. Bot. 37:879-887.
Stack, R.W. 1977. A simple selective medium for isolation of Cochliobolus sativum from
diseased cereal crowns and roots. PI. Dis. Rep. 61:119-522.
Symptoms of Pythium,
Gaeumannomyces and Rhizoctonia
Many Pythium species attack cereals. Damage in the field can be seen as stunting and
yellowing of plants. Although easy to observe, these symptoms are difficult to
distinguish from nitrogen deficiency. To determine the cause of the observed symptoms,
examine the root system; watery, atrophied brown-reddish roots indicate Pythium.
Oospores can be detected in root tissue after staining with lacto-fuchsin (0.1 g fuchsin
acid /100 mllactic acid).
Gaeumannomyees graminis var. tritiei (syn. Ophiobolus graminis), take-all
Since damage by this fungus is reduced when soil temperature goes above 27C; it may
not be important in the tropics. However, it is very important in areas with rather low
soil temperatures (10-15C). In the field, diseased plants (white heads) appear in
irregular patches similar to those caused by Fusarium. However, in contrast with
Fusarium symptoms, the lowest internodes and roots of plants affected by the take-all
fungus are shiny black in color. Also, a black mycelial network is present on the surface
of infected roots.
This fungus can cause blight and yellowing of seedlings, but in adult plants symptoms
resemble those of Helminthosporium and Fusarium. Lesions in adult plants are sharp
eyespots (strawbreaker) on the lower leaf sheaths that may weaken culms and lead to
Isolation of Pythium, Gaeumannomyces and Rhizoctonia
The technique described below works well for isolating Pythium and Gaeumannomyces
from the wheat root system. It is also useful for isolating Rhizoctonia from wheat tissue.
This technique is based on using fungal traps which consist of infected roots or other
plant tissues. For Pythium, it is best to use wheat roots collected in a field suspected to
be infected with the fungus, regardless of whether symptoms are well defined. This
condition is most often seen when plants reach maturity, and other pathogens and
saprophytes may be present in the same lesion. It is difficult to isolate Pythium and
Gaeumannomyces directly from infected roots.
Com meal agar is used to isolate Pythium and Gaeumannomyces. To prepare CMA, mix
40 g com meal in 1 L of water and keep at 50C for one hour; strain through filter paper,
add 15 g agar and sterilize. Rhizoctonia grows well on PDA.
Traps. Collect roots in the field, take them to the laboratory, and rinse them very
carefully on sieves to remove soil particles and other debris. Place this material in pots
half filled with sterile sand, and plant 4-6 wheat seeds on top of roots (Figure 14 a).
Cover with about 2 cm of sterile sand. Irrigate pots and incubate them in the laboratory
using additional light (12 hours of light). For Rhizoctonia temperature should be 20-25C,
14-16C for Gaeumannomyces, and 18-20C for Pythium. Make sure pots are well drained,
and add water as necessary.
Take seedlings from the pots 5-6 days after emergence (Figure 14 b). Remove roots very
carefully from the soil so as to preserve the original root mass. Then wash by immersing
slowly in water to obtain intact samples. If Pythium is present, infected roots will be
small and light brown in color. If Rhizoctonia is present, lesions are brown; they are black
in the case of Gaeumannomyces (Figure 14 c).
Isolation may done following one of two methods:
1. The complete root system is laid down gently on the medium in a plate. This method
is generally used when few or no symptoms are visible.
2. When severe symptoms are present, individual root segments from infected material
are cut and plated on a culture medium recommended for the suspected pathogens.
Disinfection of plant material generally is not necessary when using this method. To
avoid bacterial contamination, dry roots carefully before transferring to the medium.
The use of wheat seedlings as a selective medium facilitates the isolation of the most
aggressive and virulent pathogen present in the plant tissue, and inhibits growth of
weak pathogens and saprophytes. In both cases, inoculated plates should be incubated
upside down. For Pythium, examination of plates should start after 24 h to avoid
contamination. Pythium isolates generally produce one colony, 50-60 J.1m in diameter,
after 24-48 h. Growth of Pythium on this medium is less conspicuous than Fusarium and
is usually restricted, with little aerial development. Growth will be more visible if plates
are observed through the bottom using refracted light. If a colony with the above
described features develops after a 24-48 h incubation period, it will almost invariably
be Pythium. Re-isolations should be done at this stage by taking mycelium from the
Figure 14 a, b, c. Steps for constructing a trap for isolating fungi that cause root rots.
edges of the colony to obtain pure cultures. Fusarium, Gaeumannomyces,
Helminthosporium and/ or Rhizoctonia usually take three or more days to produce
Compared with Pythium, the initial growth of Gaeumannomyces is very slow, taking
several days to develop at this temperature. Cultures should be examined to get rid of
Identification of Pythium
Taxonomy of Pythium species is generally based on a few distinctive morphological
structures relating to the production of sporangia and oospores or conidia. The presence
or absence, size, shape and number of these structures are greatly affected by the
medium used as well as by temperature regime, age of the culture and other
environmental factors used to induce their formation. The structures on which the
identification of Pythium species is based are defined and described below.
Sporangia. Sac-shaped structures whose complete protoplasmic content is converted into
motile, asexual spores called zoospores. The time required for sporangia formation in
culture medium, as well as sporangial number and morphology, varies widely among
species. Some are formed very quickly in agar medium, while others are formed only
when the mycelium is submerged in water. Pythium basically produces three types of
sporangia: globose, lobulate and filamentous. Species with filamentous sporangia
generally produce zoospores only when submerged in water. Zoospores vary in size,
shape, and position of the flagella. However, since they are very small, only extreme
variations of the described morphological features are useful in taxonomy.
Conidia. Spherical, globose to ellipsoid structures, in most cases resembling sporangia.
The only difference is that conidia do not produce zoospores.
Oogonium. Female gametangium containing one or more gametes. Oogonia are
spherical, sub-spherical or ellipsoid, and may have spines or other protuberances. They
can be terminal or intercalary, but most species have both. Temperature, media, and the
length of time in the media are factors that affect size, shape, and the number of oogonia
Antheridium. Male gametangium. Antheridia are probably the most difficult taxonomic
feature to observe. The number of these structures may vary from one to more than 25
per oogonium. Depending on their position, they may be hypogenous (below the
oogonium) or perigenous (beside the oogonium). They may be monoclynous in origin
(antheridia are formed from any hyphal branch on an entirely different oogonial
Oospore. A sexual spore produced by the union of two morphologically different
gametangia (oogonium and antheridium). Oospores are produced individually under
normal conditions. The oospore may completely fill the oogonial cavity or the oosphere
in which it is formed; in this case it is plerotic. If it does not fill the oogonial cavity or is
free within it, it is aplerotic. Unfortunately, there are very few species which present one
condition and not the other. Sometimes, the two conditions can be observed in the same
Petri plate.
Method for inducing zoospore production
The fungus is cultured on com meal agar for five days at 15C. Small portions of the
culture (3-5 mm) are transferred to test tubes containing sterile water and fresh leaves (2
em) that have been boiled for 10 min in distilled, sterile water. After leaf infection (24 h),
transfer the leaves to Petri plates and incubate at 18-20C. Sporangia are generally
produced after 24-36 h. In some cases, periodic water changes will stimulate zoospore
Frezzi, M.J. 1956. Especies de Pythium fitopatogenas identificadas en la Republica
Argentina. Revista de Investigaciones Agricolas. T.X. 2:197-241. Buenos Aires,
Identification of Gaeumannomyces
Gaeumannomyces forms thick, black mycelium. Initially, radicles are brown in color but
tum black within 10 days. At about this time, perithecia formation on roots, crown and
lower sheaths starts.
Identification of Rhizoctonia
Rhizoctonia mycelium tends to branch at right angles and form septa near the branch
bases. The fungus produces irregularly shaped sclerotia after one week on culture
Identification of Sclerotium rolfsii
This fungus has a very wide host range and seriously affects some crops, especially in
the tropics. It typically produces white mycelial growth on the surface of soil and
plants. Sclerotium rolfsii produces sclerotia that are from white to dark brown in color
and resemble mustard seeds. Sclerotia are very easy to observe on dying plants. To
isolate this fungus, transfer mycelium or sclerotia to PDA with a sterile needle.
Nematodes, frequently referred to as eelworms, are microscopic roundworms too small
(0.3 to 5.0 ~ m ) to be observed with the unaided eye. In the past, crop damage by
nematodes was attributed to other causes, such as soil infertility or water stress.
Additionally, no clear information on nematode pathogenicity was available.
Plant-parasitic nematodes are found all over the world, and roots of virtually all plants
are infested by one or more forms. More than 5,000 species belonging to 200 genera are
known to parasitize plants and can cause economic damage to crops.
Soil nematodes: Identification
of parasitic and saprophytic species
Although nematode genera have distinctly different morphological characteristics, all
pathogenic species possess a feeding apparatus known as a stylet that enables the
nematode to penetrate plants and extract the nutrients it requires. The stylet is absent in
saprophyte nematodes.
Ectoparasitic nematodes such as Tylenchorhyrtchus, Helycotylenchus and Xiphinema
remain outside the host while feeding on its internal cells. The nematode uses the stylet
to pierce the cells, retracts it after a brief feeding period and then repeats the process. In
contrast to this type of feeding behavior, endoparasitic nematodes-including
Meloidogyne and Pratylenchus-following penetration migrate into the root tissue, where
they feed and complete their life cycle. Endoparasitic nematodes are considered more
insidious parasites since they disrupt internal tissues during their migration and are in
contact with the vascular system during feeding. A further complication with nematode
attack is that their penetration can provide portals of entry for soilborne fungi and
bacteria, thus creating secondary infections.
Important characteristics of parasitic nematodes, including the stylet, can be observed
in Figure 15.
Sampling techniques
Diagnosis of a nematode problem requires identifying the pest in association with the
diseased plant. Figure 16 shows different ways of taking soil and plant samples in areas
presenting these problems.
M o-e-m-a-tod-e-s-----s-i .... m
I,1 (often plant parasitic)
Esophageal median bulb
I proT'"
Body size
swollen, saccate V
small 1mm), large (> 1mm),
long, straight stylet
I short, cuwed stylet
MeJoidogyne vermiform
Heterodera Trich dorus stylet flanges
I distinct (evident Annulations non I-----"",absent fl1
segrm_en_ta_ti_O_n) d.,istinct l! i
Xiphinema LongLrus
Criconemel/a Tail shape

Body size
,T pre,," I
large 1mm) small (> 1mm)


' I
Hoplolaimus Aphelenchus Hemicycliophora Paratylenchus
Belonolaimus Ditylenchus Pratylenchus
Scutel/onema Radopholus
Figure 15. Key for the identification of some plant parasitic nematodes.
Figure 16. Soil sampling techniques used in diagnosing the presence of nematodes.
Methods for isolating nematodes
from soil and plant tissue samples
In the case of Heterodera or Meloidogyne, the swollen females can be observed directly on
the roots or in root galls. However, for the remaining genera, the nematodes must be
extracted from the soil or the roots. The easiest and best known technique for extracting
nematodes from soil is using a Baermann funnel (Figure 17 a). Ideally, the soil sample
should be suspended in water and passed through a series of sieves. The nematodes
and the residue can then be placed in a Baermann funnel (Figure 17 b) or extracted
using the sugar flotation technique (Figure 17 c).
Tissue on screen
Wire screen
Glass funnel
Rubber tubing
Nematodes concentrate here '
Pinch clamp--"
'-- ...." Bael'lllll1n lunnellpparatus
I. Baermennlunnel method
or. : - Beaker placed in
Beaker contents
placed in funnel Water level
i hours most
Fifter paper
level: Nematodes nematodes are
........... Wire screen
cover' "-.-....A-_Wlre screen: Sinking to recovered In 5
Nematodes moving
band"," : bottom of 8 ml water In
into water

Nematodes 1: rubber rubbing

shallow dish.
Rubber tUbing
".: ',', ;. Soil or plant moving Into water i
Beaker with soil or
tissue pieces 1 7
plant tissue pieces
b) Sieving method
Nematodes caughtlr1 fine sieve
Beaker placed
Largedebns ',:,'/" 325-400mesh diJwaterbottle
on Baermann
funnel and

fJ collected and '
discarded (30 ' ' 'Nematodes and nematodes
',' mesh sieve) residue washed
collected as
,.... ;.' .: :'.. from sieve Ir1to above
(nO<--'-c1 , . ! Water and Sift beaker

Water, line SOil,
and nematodes
c) centrifuge or sugar flotation method
Fill tube 1f2 Stopper tube
Afterlollowing step5$
oiscard lull with sugar
; :, and shake until
Fill tubes with
of sieving method,
supernatant solu11Orl . , ; pellet IS sugar solution
place beaker 0
(1 IbIl water) . ;' ',suspended 0 and centrifuge at
contents into
.. 3000 rpm for 1f2
centrifuge tubes. Spin
at 2500 rpm lor 4 min
Nematodes and debris
Sugar solu1ion


Clean nematodes
". -; ...-
, quickly bu1 flushed into dish or

gently lube for counting
:.:.: suspension
and observations
decanted into sieve
Figure 17 a, h, c. Methods for isolating nematodes from soil or plant tissue: Baermann funnel
method and sugar flotation method.
From G.N. Agrios (1978), Plant Pathology, Academic Press, Inc., with permission.
Comparing two methods for isolating
nematodes from soil and plant tissue
Set up two Baermann funnels, and compare the extraction efficiencies of a soil sample
with sieving and one without sieving. When a nematode problem is detected and it is
necessary to sample the area, use the techniques shown in Figure 17.
Identification of Meloidogyne species
The identification of Meloidogyne spp. requires using perineal sections. Figure 18 a, b, c
and d shows the most important steps of this technique.
Preparing perineal patterns of Meloidogyne females
Perineal patterns are necessary for identifying species of some genera such as
Meloidogyne. The procedure for doing this is described below.
Select galls containing mature females. Place in Petri dish with tap water. Single galls
are preferable to compound galls. Tease the root tissue apart with forceps and half spear
to remove adult females (Figure 18 a). Rupture the cuticle of the female near the neck
and gently push the body tissues out (Figure 18 b).
Place the cuticle in a drop of 45% lactic acid on a plastic Petri dish. The lactic acid
facilitates the removal of body tissues that adhere to the cuticle after trimming. Collect
10 to 20 cuticles in the drop and let them stand for 30 minutes to several hours. All cuts
with the eye knife are done on the surface of a plastic Petri dish to minimize dulling (the
knife should be kept very sharp).
Cut the cuticle in half crosswise with cataract knife. Remove the cuticle with the
perineal pattern from the lactic acid. Place it next to the drop and trim the perineal
pattern to a square (Figure 18 c). Place the trimmed perineal pattern back in the 45%
lactic acid. Cut 5 to 10 perineal patterns per sample. Thoroughly clean debris from the
perineal pattern with the help of a pulp canal file.
Transfer the perineal patterns to a drop of glycerin on a clean glass slide. Align the
perineal patterns so that they are in a straight line with the anus turned downward. The
interior surface of the cuticle must be placed against the glass. Press the perineal pattern
gently against the glass with the pulp canal file. Gently place the coverslip on the
glycerin drop. Excess glycerin can be absorbed by a piece of filter paper. If there is
insufficient glycerin, a small drop can be placed on the edge of the coverslip. Seal the
coverslip and label the slide (Figure 18 d).
a. Female being removed from root fragment. b. Excised female being ruptured and body tissue
gently removed.
c. Cuticle being trimmed around the perineal d. Completed slide.
Figure 18. Perineal patterns of Meloidogyne females.
Bacterial Diseases
Bacterial species that are pathogenic to wheat can be classified into four groups:
Xanthomonas, Pseudomonas, Clavibacter and Erwinia. The first two genera include species
that cause economically important damages. Both genera are aerobic gram negative
bacilli. Xanthomonas spp. do not reduce nitrate to nitrite and most of them produce an
extracellular, mucoid, polysaccharide, yellow substance on media containing glucose or
sucrose. Species of Pseudomonas are fluorescent (they produce fluorecein, a yellowish
green pigment) on King B medium. The genus Clavibacter is the only one characterized
by gram positive bacilli; Erwinia spp. are typically gram negative bacilli that are
facultatively anaerobic.
Most plant pathogenic bacteria are rod shaped and measure 0.6-3.5 Jlm in length and
0.5-1.0 Jlm in diameter. The cell walls of most of these bacteria are surrounded by a
dense, sticky substance. Most species have delicate flagella; some have a single
flagellum, some have a tuft at one end of the cell and others have flagella distributed
over all the cell surface.
When a bacterium multiplies on the surface of a solid agar medium, its progeny soon
forms a visible mass called a colony. Bacteria reproduce at a surprisingly quick rate;
under favorable conditions, they divide every 20 min. At that rate, a million bacteria can
be generated over a 10-h period.
Identifying a bacterial disease
Bacterial diseases are often considered difficult to manage. In some cases, they are not
easy to identify because they tend to be mistaken for physiological damage or damage
caused by environmental stress. The methodology used for isolating and identifying
bacterial diseases is very different from that used for identifying fungi; because of their
size, bacteria cannot be identified under the microscope.
What follows is a description of the procedure used for identifying a bacterial disease
taking Xanthomonas and Pseudomonas spp. as examples. In the first example,
Xanthomonas campestris pv. undulosa is used.
Attach the sample to the diagnostic sheet and describe the observed symptoms. To
confirm that the sample is infected by a bacterium, proceed as follows:
Observation using a dark field microscope. Using a scalpel cut a piece of leaf (about 3 x 3
mm) from the border between healthy and necrotic tissue. Prepare a slide with a drop of
sterile water, add the sample and place the slide cover. Observe bacterial ooze coming
out of the diseased tissue using a dark field microscope and low magnification (on the
dark field the ooze looks like a continuous flow of white dots coming out of the
diseased tissue) (Figure 19).
Isolation. To isolate species of Xanthomonas and Pseudomonas, the most important genera,
Wilbrink's and King B media are used. The ingredients and procedures for preparing
these media are as follows:
Wilbrink's medium (selective medium for Xanthomonas)
Bactopeptone 5g
Sucrose 10 g
0.5 g
0 0.25 g
(anhydrous) 0.05 g
Agar 15 g
Distilled water 1000 ml
Sterilize the medium; let cool to 45-46C and add 75 mg cycloheximide dissolved in 2
ml ethanol (75%).
King B medium (for fluorescent Pseudomonas)
Agar 15 g
Proteose peptone No.3 (DIFCO)
or polypeptone
,20 g
Glycerol 10 g or 15 ml
(anhydrous) 1.5 g
0 1.5 g
Distilled water 1000 ml
pH 7.2
Use a plate with Wilbrink's agar medium. From the border of the lesion take a piece of
diseased leaf tissue of the same size as used for observation under the microscope.
Shred it in sterile water using sterile scalpel and forceps. Soak for about 10 min. Using a
sterile nickel or chrome wire loop (if a wire loop is not available, see instructions for
making one in Figure 20 a), gently rub the agar in four dilution fields flaming the loop
and cooling it after each field as indicated in Figure 20 band c.
Incubate at 27-30
C for three days. Then observe the typical yellow mucoid colony
suspected to be X. campestris pv. undulosa. Sub-culture by dilution streaking to obtain a
pure culture (Figure 20 b). A pure colony is produced by multiplying a single cell
separated from the others through dilution streaking.
Pathogenicity test
This test is most important to determine whether the pure culture obtained is from a
pathogenic bacterium. Use young host plants of the crop where you observed the
lesion-wheat, in this case. Using a syringe, inject a concentrated bacterial suspension
prepared from a pure culture of the suspected bacteria into the stem of wheat plants.
Figure 21 a and b shows how to position the needle correctly to infiltrate the suspension
into the leaf blade.
Incubate plants for one week in a moist chamber (Figure 22). If extended lesions similar
to symptoms observed in the field are reproduced, the isolate is most probably
pathogenic. However, to verify Koch's postulates it is necessary to re-isolate the same
bacteria that was inoculated. Using the same agar medium, the appearance of the re-
isolated colony has to be the same as that of the colony initially isolated and obtained in
pure culture from the field sample.
Flame loop after each streak (1,2,3), Stop halfway, turn plate, and
then pick up inoculum by streaking continue without flaming the
through previous streak a few time loop
Figure 20. How to make a bacterial culture. a. Preparation of wire inoculating loop using 24
swg nichrome or platinum wire and a 4-mm diameter glass rod. b. Preparation of concentrated
inoculum. c. Preparation of dilute suspensions.
Source: Lelliot, RA., and Stead, D.E. 1987. Methods for the diagnosis of bacterial diseases of plants.
Figure 21. Correct (a) and incorrect (b) way of Figure 22. Host seedling incubated in a
holding the hypodennic needle during polyethylene sleeve with a wire frame to keep
infiltration of a leaf. the plant from touching the polyethylene.
Source: Kiraly et al. 1970. Methods in plant pathology. Source: Kiraly et al. 1970. Methods in plant pathology.
Budapest. p. 161. Budapest. p. 158.
Biochemical and physiological tests
After the pathogenicity test, you need to perform different biochemical and
physiological tests to determine which genus or species the isolated pathogen belongs
to. We will perform three basic tests as examples.
Fluorescence on King B medium. Take a single colony from each of the two types of
bacteria that you were given and streak them onto two different plates of King B
medium, as previously described. Observe the fluorescence after 4 days' incubation at
27C. This allows the identification of Pseudomonas spp. (Figure 23).
Nitrate reduction test. Use this test to distinguish important groups of bacteria, such as
Xanthomonas spp., that are not able to reduce nitrates. The medium used is described
Medium for the nitrate reduction test
Peptone 10 g
Yeast extract
Agar 2g
Distilled water 1000 ml
For this test, use sterile test tubes containing 5 ml medium. With a wire loop, inoculate
the medium with fresh, pure culture placing it at the bottom of the tube. Incubate tubes
for two days or more until adequate development is observed. Then add the following:
Lugol One drop
Reagent I (Greiss I) 0.5 ml
Reagent II (Greiss II) 0.5 ml
Reagent I (Greiss I): 0.8% sulphanilic acid in 5N acetic acid (the latter is prepared by
mixing 57 ml glacial acetic acid and 143 ml distilled water).
Reagent II (Greiss II): N-(l-naphtyl) bichlorhydrate 0.1% aqueous ethylendiamine.
If nitrite is present, a red spot will appear on the surface in a few minutes, and the test is
positive. If no nitrite is detected, add a small amount of zinc dust with the tip of a
spatula. If a red spot appears after a few minutes, this indicates nitrate is present in the
medium and confirms the test is negative (Figure 24).
KOH test. Use the same plates as for the first test. Place a few drops of 3% KOH solution
on a glass slide. With a needle, take some culture and quickly swirl it through the
medium. If the strain is gram negative, the suspension thickens and forms a mucoid
thread when the needle is lifted. Gram positive bacteria disperse in the drop and do not
cause this reaction (Figure 25).
Indicate whether your bacteria are gram positive or negative. Except for
Corynebacterium spp., most plant pathogenic bacteria show a negative reaction.
Figure 19. Procedure for making a
preliminary diagnosis of a bacterial
Figure 23. Pseudomonas sp. fluorescing on King B medium.
E. Duv9iller E. Duveiller
Figure 25. Detecting gram negative
bacteria using the KOH test.
Figure 24. Nitrate to nitrite reduction test.
Viruses that infect plants never leave their hosts, because they cannot survive outside
them. For this reason, viruses are not disseminated by wind or water, as is the case for
most fungi and bacteria. Transmission of viruses from plant to plant can take place
through vegetative propagation or mechanically by sap, pollen, insects, mites,
nematodes, dodder, and fungi. Plant pathogenic viruses differ from other pathogens in
their size and shape, their simple chemical makeup (nucleic acid and protein) and
physical structure, method of infection, propagation, translocation within the host,
dissemination and symptoms.
Because of their small size (measured in nanometers) and transparency, viruses cannot
always be observed or detected with the methods used on other pathogens. Methods
for detecting viruses on plants are based mainly on virus transmission from diseased
plants to healthy ones by means of sap, parasites or insect vectors. However, definite
proof that a virus is present is only possible by purifying it, observing it under an
electron microscope and/ or doing serological and nucleic acid testing.
Barley yellow dwarf (BYD) and barley stripe mosaic (BSM) are some of the most
important cereal virus diseases.
Transmission of specific variants of barley yellow dwarf virus (BYDV) by the most
important species of cereal aphids.
BYDV variants
Aphid species MAV PAY RMV RPV SGV
M. dirhodum
+ +
R. maidis
R. padi
+ +
R. rufiabdominalis
+ + +
S. graminum
+ + +
+ +
(+) Indicates aphid species reported to consistently transmit BYDV variants in trials using a single aphid. Transmission
efficiency varies depending on the virus-vector combination.
Source: Gildow, F.E. 1987. Barley yellow dwarf virus: Aphid vector interactions associated with virus transmission and
vector specificity. In: P.A. Burnett, ed. World Perspectives on Barley Yellow Dwarf. Proceedings of the International
Workshop. Udine, Italy, pp. 111-122.
Barley yellow dwarf virus
This virus is transmitted by aphids acting as vectors. Five aphid species have been
found to be the most important vectors: Rhopalosiphum padi, R. maidis, Sitobion avenae,
Schizaphis graminum and Metopolophium dirhodum. Usually called cereal aphids, they
transmit different variants of BYDV (see table).
Identification of BYDV aphid vectors
Observe the different aphids species under the stereoscope, differentiating them by
particular features such as: shape and size of the comicles, antennae length, wing vein
location and color.
BYDV transmission
BYDV transmission using aphids can be achieved following two methods, one for the
field and one for the greenhouse:
1. Aphids are collected from fields where BYD symptoms are present, and are placed
in Petri plates (seal them to avoid escapes). If they are identified as cereal aphids,
then they are allowed to feed on healthy indicator plants that have been grown
protected (with cylinders, cans, boxes, etc.), to be sure that they have not been
infested by other insects. Place aphids on leaves or sterns and cover them again
(Figure 26 a, b, c). Using susceptible varieties such as Bow'S', Black Hull-less and
Atlas 66 for inoculation is recommended. Plants are examined for symptoms a
month after inoculation.
Incubate plants in the greenhouse at 20-25C. After 72 h take out the aphids and
fumigate the plants. If the ELISA test is available, leaf samples should be taken and
analyzed eight days after inoculation to determine whether transmission was
successful and what variant was transmitted. If ELISA is not available, plants will
show symptoms of the disease 10-12 days later. In the latter case, the variant present
can only be approximated based on the specificity of the vector species/virus
variant transmission.
Figure 26 a, b, c. Steps to follow when inoculating plants using vector aphids.
2. This method is useful when a greenhouse and healthy aphids are available. Aphids
are placed in Petri plates with plant material infected with the virus on moist filter
paper or the leaf pieces are buried in moist sand to maintain a favorable
environment. Seal the plate with parafilm and place in darkness for 36-48 h. It can be
assumed that during this period the aphid has fed on the infected tissue and has
acquired the virus. Then, take the aphid out and transfer it to another plate with
healthy plant tissue so it will infect the tissue. In both cases plants of highly
susceptible varieties such as Black Hull-less should be used. Plants should kept at
20C under bright light; otherwise, symptoms will not express as they should.
Barley stripe mosaic virus
This is one of a few viruses transmitted on the seed of grass species. When barley stripe
mosaic (BSM) attacks barley, it can be mistaken for Pyrenophora graminea, since early
symptoms of both diseases are similar.
The BSM virus has been observed on barley in most countries around the world; its
distribution is so broad that it may have been disseminated through intemational seed
shipments. It has also been found on wheat and oats.
BSMV transmission
This disease is seedbome or mechanically transmitted through sap. Mechanical
transmission is one of the most used diagnostic tests, since it is efficient, sensitive,
cheap, and provides essential information for the characterization of the virus.
Viruses can be transmitted among plants of the same species or genus or even of
different genera. In fact, each virus can produce characteristic sYmptoms on a range of
plants sometimes belonging to a genus different from the natural host. These plants are
very important for diagnosis of a viral disease and are called "indicator plants". Among
the dicotyledons that have been artificially infected for use as indicator plants are
Chenopodium amaranticolor, Ch. album, Ch. quinoa, Beta vulgaris, Spinacea oleracea and
Nicotiana tabacum var. Samsum.
This type of transmission has the disadvantage that it takes several weeks before the
reaction is expressed. Even then, the virus must be successfully extracted from plant
tissue. During inoculation, be sure to injure plants slightly so the virus can penetrate.
Procedure: Wash hands with soap and water. Select indicator plants and the leaves to be
inoculated. Crush infected material in a sterile mortar with 0.5-1.0 ml distilled water.
Add carborundum (half the volume of a chickpea). With a moist finger or a cotton swab
rub the sap suspension on each marked leaf, moving from the petiole to the leaf tip,
supporting the leaf with the other hand. Do not rub the same area twice. Repeat with
each marked leaf. Immediately after inoculation, wash the inoculum from the test plant
using distilled water with an atomizer. Infection is immediate; leaves are washed to
eliminate compounds produced by the plant to inhibit infection. Incubate plants in the
greenhouse and check them every day because it is important to know the day
symptoms appear.
Detecting seed transmission of the virus
To detect the virus on infected seeds, sow seeds in the greenhouse. Incubate under good
light and temperature (around 25C) conditions so symptoms will express without
environmental stress. Symptoms start to appear when plants are at the 2-3 leaf stage or
later, depending on the original virus concentration on the seed. If concentration was
low, plants will take longer to express symptoms.
Culture media used for isolation, increase and conservation of cereal pathogens.
Fusarium spp.
H. spiciferum
H. tritici repentis
H. teres 1. teres
H. teres f. maculata
Pythium spp.
Ophiobolus graminis
syn. Gaeumannomyces
Rhizoctonia spp.
Sclerotium roltsii
Septoria tritici
Septoria nodorum
Rhynchosporium secalis
Altemaria spp.
PCNS (soil)
Corn meal agar
Czapek's modified
broth (specific)
V-8 (30%)
V-8 (15%)
Use traps (wheat
seedlings) sown in
sterile sand with
infected tissue
Use traps (wheat
seedlings) sown in
sterile sand with infected
Use traps (wheat
seedlings) sown in
sterile sand with
infected tissue
444 yeast-peptone
Lima bean agar
Increase Conservation
Chinese bean medium Sterile wheat grain
Pieces of sterile maize Sterile soil
PDA Sterile wheat grain
Czapek's modified
broth (specific) Infected
Czapek's broth leaves
PDA Sterile wheat grain
V-8 (30%) Infected leaves
V-8 (15%) Infected leaves
Corn meal agar Wheat leaves
in sterile water
Corn meal agar Sterile oat grain
liquid medium 4-44 medium
yeast-peptone Leaf medium
444 yeast-
peptone medium
Medium for Medium for
Septoria nodorum S. nodorum
Lima bean agar Lima bean agar
ISBN: 968-6923-82-9
International Maize and Wheat Improvement Center
Centro Internacional de Mejoramiento de Mafz y Trigo
Lisboa 27, Apartado Postal 6-641,06600 Mexico, D.F., Mexico